Before I decided to go with a MegaSquirt I contacted as many people as I could about reprogramming my chip or purchasing a different ECM and/or memcal. I'd recommend contacting a couple of these guys and tell them what you have in terms of parts and ECM.
Sinister Performance, LLC.
Tuned Port Injection
Both Sinister Performance and Scott Hansen were more than helpful. I would be relatively confident that either would be willing to help and let you know what you might have occurring that is causing some of your problem.
Also, here a couple of links with a lot of helpful info about using a stock TPI setup with a stock ECM in a non TPI chassis :
TPI Conversion Parts
Hot Rod Handbooks: Tuned Port Fuel Injection
Programming PROMs for your Thirdgen Fuel Injected F-Body: Part I - ThirdGen.org
I think you'll discover that there a lot of guys on the thirdgen site that have done the conversion that is in your car. There is a bunch of great info on the ChevyThunder site and in the hot rod handbook site. You might also find that one of these guys can direct you to someone in your area that could help you out.
Spend a couple of hours reading and a week or two picking the brains of the guys that have done the conversion and you will probably figure out the problem with your car or at least find out what you have to do inorder to get your problems resolved.
As always - good luck.
PS - your car is one good looking ride with a really cool looking setup under the hood