What year and configuration of Dakota did the PCM and harness come out of? A 5.9L engine wouldn't have been in front of a 42RE transmission...probably a 46RE. As I understand, the 46RE is a bit different from a 42/44RE, and the harness/PCM pinouts may be different.

 

I believe the pin-outs for the 3.9/5.2/5.9L transmissions (42RE/46RE) are the same.
Yes, on the transmission and overdrive assembly, there are three electrical connectors.

For some more troubleshooting procedures, go here. It's actually for the 1996 Dakotas, but the basic troubleshooting steps remain the same.

 

I don't know if this helps you at all, I'm in the middle of swapping transmissions for my V6. I have a friend that works at a dealership for dodge/chrysler tell me that a 42re will only work right behind a 3.9. Any V8 would have had the 46re. And that dodge also changed transmission electronics between model years, So I had to find one that was from a '97 model year. I may be wrong, but just forwarding the info I was given. I don't think the electronics match up and that could be why.

 

He may be right about the 42RE only working behind a V-6, but he's not right on the V-8 transmission. Most V-8 trucks had the 44RE. The 5.9 R/T had the 46RE. The first number is the number of gears (4) and the second number is the relative strength (1 being low, higher numbers being stronger). The 44RE is stronger than a 42RE, and a 46RE is stronger than the 44RE.

 

I had it all working, but something happened. I think it short circuited, would that cause it to go into limp mode...?