is the computer for a auto trans different then the 5sp man trans. besides making the trans shift, timing,fuel,etc. i change over my truck 96 crewcab from a e4od to zf5sp and now the truck just doesnt have the power it had before and i lost about 5lbs of boost

 

Yes, I believe that it's looking for feedback from the tranny that it's not getting. Not sure how that gets fixed unless you have it reprogrammed or replace it with one that originally had a manual tranny.