UPDATE!
FINALLY got the trans off and it turn out that it was the issue.
The motor spins VERY smooth with the Flywheel and Torque Convert installed and no trans!
I have a spare that I am rebuilding and upgrading.
Got the transGo HD2 shift kit and new gaskets to go on the low mileage KA trans and hopefully just easily swap the bellhousings.
Then I am having a local shop install it, not taking any more chances and it's a HUGE PITA!!