Ok, I am going to list some of the things that I have had issues with before, see if maybe any of these could be you.
Even if you did not have the TC all the way seated to the pump, the transmission would more then likely come close to bolting to the motor, but the TC would be pinched between the flywheel and transmission. Are the TC studs properly going thru the flex plate? My new Ebay flex plate this year had one hole that needed a little "massaging" to get the TC studs to all come thru the flex plate freely. Those few threads catching on that hole held me up.
If your studs are coming thru nicely, then something has to be catching it. But my get is the TC studs are not perfectly fitting your flex plate. Here is another thing I have done while installing my autos. When you have the studs of the TC pushed thru the flex plate, grab one of those studs, and wiggle it clockwise and counter clockwise. It should move freely back and forth and make a nice little "ting" noise on the flex plate. If not, something is binding.
As I say all this, then think about a c-6 I messed with last summer. It may have had bolts that screwed into the TC vs. studs mounted in the TC. If this is the case with you, I am not really sure what it would be. Is the hub on the front of your TC too big to go into the flex plate? Just grasping here now…..
Also, make sure you put that aluminum shield in there between the flex plate and the engine. I have forgotten that a time or two
Let us know,
Ryan