You will get all sorts of codes from the auto being missing. You will have to ground out your neutral safety switch wire, and you will be lucky if the motor runs right with all the codes it will throw. The only way around it is a manual PCM, maybe the TCM too, not sure if the manual trans had one or not. And you will want to get the proper wiring harness. The mod CAN be done, you will just need a donor Dakota as well as some money to program the PCM at the dealership. Time will be a huge factor too. You may get some gruff about putting a Dakota PCM into a Durango, but unless someone here has some input as to why not, I say, why not? Do it, and if it works, hell ya. If not, sell the PCM on Craigslist or something. As long as you get the PCM programmed for your BCM and everything, theoretically it should work right?
I speak out of theory on this subject. Anyone who has experience is free to prove me wrong