I doubt your rig has a TH400 in it. TH400's use an electrical kickdown under the dash. That trans is NOT interfaced with the ECM in any way so the PROM replacement has dick to do with trans shift.
If your unit uses a kick down cable that affects the shift pattern it may well be a TH700 or TH200 application. They require the cable to be installed so that internal trans pressures are correct. Without it the trans will die.
Sounds like the shop trying to solve your problem needs to go back for some schooling. They seem to subscribe to the old hotrod school, "if one doesn't understand it remove it" and say "nothing can be done about the problem" or 'it will run better without it". Definitely unprofessional. All to many of these types still around.
Don't try to diagnose your problem over the net, you end up getting nothing but guesses at a repair because those involved can't test or drive the rig. You wouldn't take medical advise over the net, why automotive diagnostics. Take it to a reputable tranny shop. You may well have had problems with the trans before you swapped motors, but it took the increased torque to bring the problem to the surface.