I have been through the same thing with my F-Body car and finally called Ed Quay. After talking with him we were able to solve the problem.
Had (2) problems, The pinion shaft of the rear end was not in line with the crankshaft and I also had to install limiters on the engine block to the subframe to stop the front to back motion of the engine. It didn't make sense to me at first but Ed told me the transmission was breaking when I let off the gas. Well that has been about 10 years ago and I haven't broke one since. Maybe you will be as lucky.