I work for one of the biggest part suppliers in the industry, and i can tell you that there are 6 different PCM part numbers for my 2002 and they DO require flash re-programming (VIN and Miles) on or off the vehicle. The normal way to determine the one you need is to match up the OE PCM's part number. In your case, thats not as important as these key things that do matter: Engine, Transmission, Emissions System, Mileage, VIN.
I've also personally done PCM replacements and Instrument Cluster replacements. Vin and Mileage matter. The data for each are stored BOTH in the PCM and the Instrument Cluster. If the PCM has a conflict with the same data stored in the Instrument Cluster, it will go into Limp Mode. Example: forget the motor swap for a moment. Pretend your Dak has 200,000+ miles on it; you could go to the scrap yard and buy a instrument cluster out of a Dak with only 70,000 miles on it and swap it into your truck and put it up for sale. Nope. Believe me, the manufactures have thought of this, and if it were that easy to manipulate the mileage on a vehicle, everyone would be dong it. This isn't the 1960's. If you try that, the mileage (and VIN) stored in the PCM will have a conflict (a non-match) with the miles stored in the cluster and the truck goes into limp mode. Its the same with a VIN conflict.
In short, some flash re-programming will be needed so that your cluster and PCM have matching VIN and Miles, and you need to get the PCM that matches up with your Engine, Transmission, and Emissions System combination.
Yes, obviously, most the emissions system comes over with the engine, but what about your exhaust? If your Dak is 49 state federal emissions equipped and thats the cat converter still on it, if you match it up with an engine and PCM from a California emissions equipped engine and PCM, you re going to have CEL (Check Engine Light) issues. The software on the California equipped PCM will be looking for a higher level of emissions performance than your 49 state converter can provide and you will end up with P0420 codes (Catalyst System Efficiency Below Threshold).
You can find the emissions info on a white 2x5 inch sticker stuck to the underside of the hood of your DAK (assuming it still has the original hood). There is a paragraph on that sticker that will tell you the emissions its equipped with. There are only 2 systems; "49 state Federal" -or- "49 state Federal AND California".
The easiest thing I can think of is; get the Engine, Transmission, Trans Control Module (dont forget that) and PCM all from the same donor truck. However, the PCM will need to flashed to match the VIN and Miles of your DAK. Check the emissions info sticker under of the hood of your donor truck (assuming it still has the original hood) and hopefully it matches your Dak. Otherwise, you may also need to swap a cat converter onto your Dak that matches the emissions of the donor Engine/PCM.
You may also need to match up the O2 Sensors to the right emissions system as well.