Ok well here's what I got. I got a 1993 dodge Dakota with a 318 multi port in it. Truck ran like a raped ape. No issues out of it but the frame and body were in real bad shape. So I got a 1989 Dakota 4x4 with a 3.9I v6. This truck also had No issues. I just want happy the power it had or should I say 'power it didn't have'. So I I pulled the 318 32nd stuck it in the 89. The swap want ok. I changed out fuel tanks also and obvously kept the wire harness and computer with the v8. I have since then replaced plugs wires cap button coil crank censor and exohaust from manifolds back. But now it don't want to run worth a crap......?

 

Based on what you say I would check all of the wiring connections then go through it as if you just rebuilt it and set all the settings you would set to the spec and go from there. Since it runs it seems like it has to be something adjustable.