2001 Dakota 3.9l 5spd to 5.2l 5spd swap!

6129 Views 30 Replies 7 Participants Last post by MikeyBoiTV, 4 mo ago

MikeyBoiTV

Discussion Starter · Jun 3, 2021

Well guys this is my first post on a forum ever about one of my builds. My latest build is this 2001 Dakota 3.9l 5spd manual. I was working in a salvage yard at the time and had 3 donor trucks to choose from. I bought this one for 300 dollars because of its immaculate condition given how long its sat. First thing i wanted to do was obviously put a v8 in it! I had assumed that the swap would be fairly simple since the trucks were so identical but later on in the build i discovered how different they really are. The main donor truck that i used for the motor was a 97 5.2l extended cab automatic. The others were also 5.2l but the motors were in questionable condition. The motor i decided to go with was the one that i could get running. So far the truck has been completed but ive run into one problem that has halted the build for a couple of months due to not having the time to work on it until now. I am currently stuck with a PCM issue. The original PCM is for a 3.9l 5spd 2001 model and the PCM i planned on using was from the 97 5.2l automatic. When using the 5.2l pcm the truck fires up no problem but dies immediately. Originally i thought it was a skim issue but this truck is not equipped with one. I decided to get it flashed and programmed for my 2001 but it still does the same thing. it took me a while to notice that there is a No Bus code so thats when i figured that the 97 pcm is just not going to work. So now im stuck because the 5.2l was not produced in 2001 and up on dakotas. I read somewhere that someone used a 2001 5.9l pcm to correct this but finding one at a decent price has been an issue so now im trying to research all of my options before putting down more money on a pcm than what i paid for on the truck lol Im sure someone out there has done this exact swap before and this PCM issue is the only thing that is stopping me! Btw with the v6 pcm on it will run but not on all 8, but with the v8 pcm from the 97 it fires up perfectly but dies immediately. Anyone have any wisdom of experience for me? This issue is the only thing i have left to finish on this truck! I would love to make a post of the entire build with plenty of pictures and info when im done but i dont want to post anything until i can resolve this issue! Help me out Dakota Gods!

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NoUsername

· #2 · Jun 27, 2021

MikeyBoiTV said:
Well guys this is my first post on a forum ever about one of my builds. My latest build is this 2001 Dakota 3.9l 5spd manual. I was working in a salvage yard at the time and had 3 donor trucks to choose from. I bought this one for 300 dollars because of its immaculate condition given how long its sat. First thing i wanted to do was obviously put a v8 in it! I had assumed that the swap would be fairly simple since the trucks were so identical but later on in the build i discovered how different they really are. The main donor truck that i used for the motor was a 97 5.2l extended cab automatic. The others were also 5.2l but the motors were in questionable condition. The motor i decided to go with was the one that i could get running. So far the truck has been completed but ive run into one problem that has halted the build for a couple of months due to not having the time to work on it until now. I am currently stuck with a PCM issue. The original PCM is for a 3.9l 5spd 2001 model and the PCM i planned on using was from the 97 5.2l automatic. When using the 5.2l pcm the truck fires up no problem but dies immediately. Originally i thought it was a skim issue but this truck is not equipped with one. I decided to get it flashed and programmed for my 2001 but it still does the same thing. it took me a while to notice that there is a No Bus code so thats when i figured that the 97 pcm is just not going to work. So now im stuck because the 5.2l was not produced in 2001 and up on dakotas. I read somewhere that someone used a 2001 5.9l pcm to correct this but finding one at a decent price has been an issue so now im trying to research all of my options before putting down more money on a pcm than what i paid for on the truck lol Im sure someone out there has done this exact swap before and this PCM issue is the only thing that is stopping me! Btw with the v6 pcm on it will run but not on all 8, but with the v8 pcm from the 97 it fires up perfectly but dies immediately. Anyone have any wisdom of experience for me? This issue is the only thing i have left to finish on this truck! I would love to make a post of the entire build with plenty of pictures and info when im done but i dont want to post anything until i can resolve this issue! Help me out Dakota Gods!

Ditch the pcm and go to a megasquirt

Reactions: 1

NoUsername

· #3 · Jun 27, 2021

Or a swap to a carb lol

Reactions: 1

WaterMover77498

· #4 · Jun 29, 2021 (Edited)

I did this on my son’s 2000 that have a V6. We used a 5.2L and PCM from a Durango.
A question for you: did your truck have a security system? Did it have powered doors and locks? These questions will help me with the next statement I will make. There is an orange and green wire on the CTM that you need to ground(what most manufactures call a body control module). The CTM is behind the glove box. You might need to do more than just ground the wire. Based on your answers, I can help you the rest of the way. My son’s truck took a couple more modifications, but it worked.

Reactions: 2

MikeyBoiTV

Discussion Starter · #5 · Jul 7, 2021

Well i couldnt get a response soon enough for my patience to run out lol But what i did was just order a new PCM from ebay for a 5.9l for my exact year of truck which was 2001, only problem is that it was for an automatic. Fired right up and stayed running strong. But i did not notice immediately that it had a misfire, i put my scanner on and its misfiring on 4 and 6. So im busy as hell trying to diag that and i have also noticed that the rev limiter is limited to 3k rpm which blows. Aside from that the truck does not have a security system, its the most basic of basic models with no SKIM or anything like that. What i assume was happening is that the BCM was only willing to work with the same year of PCM that the truck was. Everything else i tried was a different year. So the no start issue is resolved, now i need to figure out why i have two consecutive misfires and where to go and get it tuned for a manual transmission because my trans temp light is constantly on and that 3k rev limiter is no bueno lol Thank you for the replies so far! But yeah the quick fix was just a 5.9l R/T PCM for the exact year model i have and that was the magic fix.

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MikeyBoiTV

Discussion Starter · #6 · Jul 7, 2021

5

Visual progress Update!

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WaterMover77498

· #7 · Jul 8, 2021

MikeyBoiTV said:
Well i couldnt get a response soon enough for my patience to run out lol But what i did was just order a new PCM from ebay for a 5.9l for my exact year of truck which was 2001, only problem is that it was for an automatic. Fired right up and stayed running strong. But i did not notice immediately that it had a misfire, i put my scanner on and its misfiring on 4 and 6. So im busy as hell trying to diag that and i have also noticed that the rev limiter is limited to 3k rpm which blows. Aside from that the truck does not have a security system, its the most basic of basic models with no SKIM or anything like that. What i assume was happening is that the BCM was only willing to work with the same year of PCM that the truck was. Everything else i tried was a different year. So the no start issue is resolved, now i need to figure out why i have two consecutive misfires and where to go and get it tuned for a manual transmission because my trans temp light is constantly on and that 3k rev limiter is no bueno lol Thank you for the replies so far! But yeah the quick fix was just a 5.9l R/T PCM for the exact year model i have and that

MikeyBoiTV said:
Well i couldnt get a response soon enough for my patience to run out lol But what i did was just order a new PCM from ebay for a 5.9l for my exact year of truck which was 2001, only problem is that it was for an automatic. Fired right up and stayed running strong. But i did not notice immediately that it had a misfire, i put my scanner on and its misfiring on 4 and 6. So im busy as hell trying to diag that and i have also noticed that the rev limiter is limited to 3k rpm which blows. Aside from that the truck does not have a security system, its the most basic of basic models with no SKIM or anything like that. What i assume was happening is that the BCM was only willing to work with the same year of PCM that the truck was. Everything else i tried was a different year. So the no start issue is resolved, now i need to figure out why i have two consecutive misfires and where to go and get it tuned for a manual transmission because my trans temp light is constantly on and that 3k rev limiter is no bueno lol Thank you for the replies so far! But yeah the quick fix was just a 5.9l R/T PCM for the exact year model i have and that was the magic fix.

I’m glad it’s running for you now.
Out swap used a PCM from an automatic onto a manual too. We have all the DTCs one would expected in that situation, but never experienced any rev limiter problems below normal levels.
Let the group know what you find!
On the misfire: have you replaced the crankshaft position sensor? This could help. From my experience, don’t go with the cheapest sensor you can find on RockAuto. It just didn’t do the job.
You might not want to hear this: but have you checked compression on cylinders 4&6? Just something to rule out.

MikeyBoiTV

Discussion Starter · #8 · Jul 8, 2021

WaterMover77498 said:
I’m glad it’s running for you now.
Out swap used a PCM from an automatic onto a manual too. We have all the DTCs one would expected in that situation, but never experienced any rev limiter problems below normal levels.
Let the group know what you find!
On the misfire: have you replaced the crankshaft position sensor? This could help. From my experience, don’t go with the cheapest sensor you can find on RockAuto. It just didn’t do the job.
You might not want to hear this: but have you checked compression on cylinders 4&6? Just something to rule out.

Yeah when i pulled the motor from the other truck it was running really nice and strong, didnt start misfiring until i swapped it to the other truck. So its either something with the tune or a bad plug wire or something really stupid lol But now that you mention it, the crankshaft position sensor, i had to use the one from the v6 because the one from the v8 didnt clear. I wonder if there is a difference between the two. I dont have any DTC's other than trans temp and misfire for 4 and 6. Gonna do some more research on the crankshaft position sensor.

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WaterMover77498

· #9 · Jul 9, 2021

WaterMover77498 said:
you

MikeyBoiTV said:
Yeah when i pulled the motor from the other truck it was running really nice and strong, didnt start misfiring until i swapped it to the other truck. So its either something with the tune or a bad plug wire or something really stupid lol But now that you mention it, the crankshaft position sensor, i had to use the one from the v6 because the one from the v8 didnt clear. I wonder if there is a difference between the two. I dont have any DTC's other than trans temp and misfire for 4 and 6. Gonna do some more research on the crankshaft position sensor.

Yes, do look closer at the sensors. In our case, the PN is different between the manual and automatic transmission. I believe the sensor that goes with the automatic was slightly longer. In any case, it rubbed on the “timing ring” (I’m sure there is a more correct term) until we figured out that was the slight whirling sound we were hearing.
Good luck! Glad you are confident the engine was running well before.

radioactive

· #10 · Jul 9, 2021

Typically once the sensor hits the flywheel teeth, it's toast and must be replaced.

MikeyBoiTV

Discussion Starter · #11 · Jul 9, 2021

radioactive said:
Typically once the sensor hits the flywheel teeth, it's toast and must be replaced.

Definitely correct on that one, but i made sure it had clearance before i buttoned it all up

MikeyBoiTV

Discussion Starter · #12 · Jul 9, 2021

WaterMover77498 said:
Yes, do look closer at the sensors. In our case, the PN is different between the manual and automatic transmission. I believe the sensor that goes with the automatic was slightly longer. In any case, it rubbed on the “timing ring” (I’m sure there is a more correct term) until we figured out that was the slight whirling sound we were hearing.
Good luck! Glad you are confident the engine was running well before.

Yeah whenever i was sizing up parts during build and fitment i noticed that the automatic crank sensor was way too long with the new manual flywheel i got so i put the v6 crank sensor and it fit perfectly. But i dont know if there is a difference between that sensor and one for a v8, so i might get another crank sensor for the v8 auto and just shim/spacer the sensor for clearance and see if it runs right. Its strange to think that the original sensor with the last manual flywheel would be different other than depth/distance from the flywheel but its worth a shot, even though its a pain in the ass to get to lol Appreciate all of your insight so far, do you have a thread for your build i can glance over? Honestly i wish i would have just went with a 5.9l to make things easier but i love the 318s so i just gotta massage it all together.

WaterMover77498

· #13 · Jul 9, 2021

Radioactive: I know, I was shocked it kept work. Not only did it have groves worn into the plastic, but the bracket was bent over a little. I guess it showed me all parts are not created equal.

WaterMover77498

· #14 · Jul 9, 2021

MikeyBoiTV said:
Yeah whenever i was sizing up parts during build and fitment i noticed that the automatic crank sensor was way too long with the new manual flywheel i got so i put the v6 crank sensor and it fit perfectly. But i dont know if there is a difference between that sensor and one for a v8, so i might get another crank sensor for the v8 auto and just shim/spacer the sensor for clearance and see if it runs right. Its strange to think that the original sensor with the last manual flywheel would be different other than depth/distance from the flywheel but its worth a shot, even though its a pain in the ass to get to lol Appreciate all of your insight so far, do you have a thread for your build i can glance over? Honestly i wish i would have just went with a 5.9l to make things easier but i love the 318s so i just gotta massage it all together.

I hate to say we didn't find this forum until we were looking for the solution to the "fire up for a couple of seconds, then quite issue" you had. As such, we never made a thread about our swap.

WaterMover77498

· #15 · Jul 9, 2021

MikeyBoiTV said:
Yeah whenever i was sizing up parts during build and fitment i noticed that the automatic crank sensor was way too long with the new manual flywheel i got so i put the v6 crank sensor and it fit perfectly. But i dont know if there is a difference between that sensor and one for a v8, so i might get another crank sensor for the v8 auto and just shim/spacer the sensor for clearance and see if it runs right. Its strange to think that the original sensor with the last manual flywheel would be different other than depth/distance from the flywheel but its worth a shot, even though its a pain in the ass to get to lol Appreciate all of your insight so far, do you have a thread for your build i can glance over? Honestly i wish i would have just went with a 5.9l to make things easier but i love the 318s so i just gotta massage it all together.

One more thought about getting to this sensor:

We removed the plastic fender liner and left it off when doing the swap. It's probably the wrong thing to do, but we haven't seen any ill effects.

With this fender liner off, and the passenger side wheel removed, this sensor isn't as bad to get to.

MikeyBoiTV

Discussion Starter · #16 · Jul 9, 2021

WaterMover77498 said:
One more thought about getting to this sensor:

We removed the plastic fender liner and left it off when doing the swap. It's probably the wrong thing to do, but we haven't seen any ill effects.

With this fender liner off, and the passenger side wheel removed, this sensor isn't as bad to get to.

I am able to get to the sensor from up top by just reaching over the passenger head with enough clearance. That being said though, i have made a discovery. In the past i looked specifically for a crank sensor for a 97 5.2l 5spd manual. Last year that was not an option for parts stores but the Autozone i went to today just showed me there is an option to get a crank sensor for a 97 5.2l manual trans...... So i have that ordered, wont be here until 4pm today so even if it does not fix the misfire, i will at least know i have the right part! lol It was actually a little exciting seeing there is a sensor specifically for this setup!

MikeyBoiTV

Discussion Starter · #17 · Jul 9, 2021

WaterMover77498 said:
One more thought about getting to this sensor:

We removed the plastic fender liner and left it off when doing the swap. It's probably the wrong thing to do, but we haven't seen any ill effects.

With this fender liner off, and the passenger side wheel removed, this sensor isn't as bad to get to.

Oh i also have the entire build process recorded on video so once the build is complete ill edit and post it with lots of details!

MikeyBoiTV

Discussion Starter · #18 · Jul 10, 2021

Well finally the Crankshaft Position Sensor came in this morning and i got it installed. Did not fix the misfire but im glad i swapped it out because the other one looked like it actually made a tiny bit of contact and this one looked perfect. So im still searching for the elusive misfire, its possible that the 5.9 R/T ecm i got for it just might be the wrong tune so im going to look around and see if there is a tuner shop or something around me that could check it out.

MikeyBoiTV

Discussion Starter · #19 · Jul 11, 2021

ALRIGHT so progress update. Today i decided to cover and backtrack my work. I found that i had two 02 sensors unplugged, no big deal. Then decided to do spark test and compression test, both were near perfect. I pulled the plugs for the misfiring cylinders 4 and 6 and i dont see or smell any fuel and there are no traces of combustion either. So i see that there is no fuel getting to the cylinders. Here is the catch, the injectors for 4 and 6 are brand new. I also had the old ones tested and they were confirmed to be perfectly fine. I put a meter on all of the injectors and every single one of them are reading the same...... So im kind of at a loss right now. For now im going to do alot of research and try to come up with something else to test. What i need to know if the fuel injectors are a constant flow rate to all cylinders or are they timed/sequential. If theyre constant then i dont understand why fuel is not getting to the cylinders, if not then i might have a bad tune. Still strange how this is playing out so far lol But slightly entertaining.

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WaterMover77498

· #20 · Jul 11, 2021

MikeyBoiTV said:
ALRIGHT so progress update. Today i decided to cover and backtrack my work. I found that i had two 02 sensors unplugged, no big deal. Then decided to do spark test and compression test, both were near perfect. I pulled the plugs for the misfiring cylinders 4 and 6 and i dont see or smell any fuel and there are no traces of combustion either. So i see that there is no fuel getting to the cylinders. Here is the catch, the injectors for 4 and 6 are brand new. I also had the old ones tested and they were confirmed to be perfectly fine. I put a meter on all of the injectors and every single one of them are reading the same...... So im kind of at a loss right now. For now im going to do alot of research and try to come up with something else to test. What i need to know if the fuel injectors are a constant flow rate to all cylinders or are they timed/sequential. If theyre constant then i dont understand why fuel is not getting to the cylinders, if not then i might have a bad tune. Still strange how this is playing out so far lol But slightly entertaining.

Good to see you are still in good humor about this!
Do you have one of these or know where you can borrow one? It won’t help you fix much of anything, but it could help you confirm/deny if those injectors are getting a signal from the PCM.

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