I just had my transmission rebuilt along with a rebuilt Torque Converter. When the TC is seated all the way against the pump, how much distance should be between the TC mounting bolts and the Flexplate?

With the transmission bellhousing all bolted up to the engine block and the TC is seated all of the way up against the pump there is approximately 1/4 inch of space.

 

Sounds a little tight, maybe on the low side of recommended clearance.
Are you sure it's seated?
Shoud fit into the notches on the pump - as you turn it, you'll feel it 'seat' - and go in about an inch.
I usually put a film of wheel bearing grease on the shaft to avoid wasting the seal, too!

 

If you can spin the converter without it dragging on the flexplate before you bolt it up, you're fine. Typically with the converter up against the pump you can barely get a finger in between the converter and the inside of the bellhousing