This is my exact situation with my truck. I bought a 2001 engine put it into my 2000 truck. The diesel performance shop had my truck for a year and couldn’t figure out why it wouldn’t run right. I finally took to the forums and found one post that said you had to have the ecm and wiring harness from the same year as the installed motor. So after a year and a half I finally bought a2001 harness and a 2001 ecm. $523 for harness with 1year warranty. $699for ecm with $200 core and 1year warranty. Looks like I might also need to buy the pcm and map sensor. It’ll be worth it to get my 650 hp truck on the road again!
Thanks for this post! It was extremely helpful!