Flexplate and TC parts numbers look good for your combo. But, it still could be a bad TC. Are all the TC bolts in place and the same size heads?
Next to investigate is:
- Damper.... is it the right one? It should have letters cast into it that say something like: "For 360 only...." etc. (As far as i know, the damper is the same for auto and manual trans, BTW.)
- Pull off the belts and idle it and see if anything changes just to eliminate that.
- The thought about the recess in the back of the crank is a good one. If it was not machined out for the nose of the auto trans TC, then the bolt up of the TC to the flex plate will be all hosed up. When you mated the trans to the engine, you should have been able to pull the TC right up to the flex plate with your fingers alone and with no real resistance. If there was a gap between the TC and flax plate that you had to close up by pulling in the TC bolts, then that is a bad scene.
- We need to know what pistons were used; the statement of ".040 over flat tops" indicates that they are not stock replacement pistons. If lighter hypereutectics, then the crank and rotating assembly will be out of balance if it was not re-balanced. Were the original rods re-used?