swapped 1997 pcm for 1998 pcm , now misfire on and 8

I have found that I cannot tune PCM's on 1996-97 PCM's because there are internal differences between them and a 1998. So I have changed 1997 trucks to a 1998 PCM before so that I can tune them.
however on the one I am working on right now is a 1997 and I have switched it to 3 different 1998 PCM's attempting to tune it. everytime I switch it to a 1998 PCM it starts misfiring on cylinders 4 and 8. but it runs fine on the 1997 PCM.
Any ideas?
also this truck has before converter from a automatic to a manual. I have tried setting the PCM up for manual transmission and automatic, same results either way

You may just need to add some changes to the misfire area for cyl 8. Just detune it a tad. Maybe the newer pcm has tighter tolerances than the older pcm. It maybe detecting a slightly weaker cylinder easier than the older pcm. Just a thought.

Between '97, '98 and '99 there may have been some wiring changes that require reassigning the proper pins. When I put a '00 0411 pcm in my '98 trans am I had to relocate almost all of the pins in the connectors. This required lengthening about half of the wires.

Google the pcm pinouts for both pcm numbers you have and it will become clear what you have to do.

Edit: Here's a thread dealing with your issue.

http://www.hptuners.com/forum/showth...-vortec-trucks