Wonderful! I can actually answer this question from experience.
What happens when you pull off the door panel, you can't really disconnect the rod, so it hangs about while you do things (I, too, installed some pretty good speakers for my Dak) and it bends the rod into shapes. The first time I did this, it took me about 2 hours to even understand why my door wouldn't open.
The rod which controls the locking mechanism also controls whether the doors close or not, and whether the doors lock or not. You'll have to do a TON of trial and error until you get it correct again (pulling the bar, AND ONLY THE BAR). Do not, I repeat, do not pull the entire thing in different ways or you'll be spending a small fortune replacing the entire mechanism. Pulling it up tightens it, but if you pull it up too much, there won't be enough force to lock it. Keep doing trial and error until you get it correct.
If you see the red marker when you try to lock it, you'll have to pull the rod up more. There should be little red showing from the door locking switch thing (sorry for the lack of better words) since you can't really align it completely and perfectly now.
Align the rods, put the panel on, and test. You might get it right when the panel is off, but when you put the door panel on, it might readjust and you're back to the original problem, which means you'll have to take it off again, and adjust until it's perfect. Allocate about 30-45 minutes, or if you're very lucky, 5 minutes.
When you finish, use the key to unlock and lock, and also use the locking switch to unlock and lock. Keep your key on you AT ALL TIMES while you do this. If you lock the door, and use the keys to unlock, and it doesn't open, go over to the passenger side and use the door handle to unlock the door, and try again. It's all about trial and error.
This has happened to me three times now, so it's best you do everything you need to do, so you never have to take the door panel off again.
Good luck!
