The bolts contacting the TC and leaving dimples, and flex plate warp are true signs of TORQUE CONVERTER BALLONING....the converter was not designed for HIGH RPM.......This can also be aided by high heat.
Is the converter painted? If the paint is flaking, this is a sign of high temp and is not good. I would talk to the converter house again or advise Alan (dirtyd0g) here about the issue, as he is the converter guru.
However, when this happens it can do hurt some things.
-Input shaft wear, the balloning SUCKS the middle of the TC in and creates LESS room for the input shaft to rome, if you have a One PEICE setup, it should be fine, if you have a 2peice....you should pull the input shaft and inspect the tip where it rides on the output/dirrect drum.
For the most part, converter ballon will not hurt the pump, since the snout of the pump is SUCKING OUT of the trans due to centrifugal forces, accualy freeding up space for the pump gears to run.
If the pan has no flakes or debris....i would be confident that the pump is just fine. However, I can't argue with inspection if you want to do that.
You need to solve the cooler flow issue, possinly track how hot the ATF gets also...you need to stay under 190.
------------------------- Dan Gilsdorf ---------------------------