So I figured out the issue; well, I was told by the manufacturer what the issue is. Most flexplates aren't specifically made for the TC of an AOD trans; they are made to fit a C4; which is a tenth of an inch off. I had to ream the mounting holes out to 29/64" to get it to fit, dry. When I mounted the engine and trans together, it still gave me trouble. So I separated the engine and trans and rotated the engine and remounted a few times until it lined up on the 3rd try. Then I got my end play. This may be atypical for this engine/trans combo; but this is what I had to do.
Now I have to deal with installing the small block and trans into a full-sized car. Getting the old engine and trans out was easy; putting them back in is another story altogether.