You may want to be sure the torque converter can be moved a short distance back from the flex plate after the bellhousing is bolt up. If not, the converter is either ballooned or is not properly seated in the pump. It is also possible that the converter is ballooning under load. Some rebuilders have a way of checking that. It may also be possible that a snap ring inside the trans has failed allowing the input shaft to be pushed forward under some operating conditions. There have been a couple of snapring TSB's in the transmissions but, I do not know all of the possible ramifications of a failure. Maybe someone here has a bit better knowledge of what happens. If you have clearance as above and you know the internal engine clearances are good, I see little else that could be a problem.