I would be checking out your mounting plate if you did not get all the bolts in proper, I am surprised it has not cratered before.
I am thinking Torque converter bolts, but now I reread, you mean transmission bolts ? you flex plate still could be buggered.
If you had the motor pulled down as far as you did , why not just go the rest of the way and pull the heads , and look at the cam. sounds kind of bearing to my old yrs.
I have not had one of these motors in any of my trucks.
Now that I had a coffee, I think you where talking about exhaust bolts.
Just read some more, sorry about the hand, take care, the truck will wait.