Are you using the TC that was in the transmission originally, or one that came with the new motor?
If you're using a different TC, it's possible the "new" one is bad. If not, you're probably onto something when you mention fluid levels. A torque converter is a stator motor; basically one side spins and draws in fluid, which in turn spins, moving the other side with it. If there's not enough fluid, it simply won't turn the other side as fast. Given that you're getting no motion whatsoever, it's either completely or almost completely dry, or as you said, not seated correctly.
I've personally never removed or installed an automatic transmission (though I have done some off-vehicle repairs, it wasn't my trans and I didn't have a hand in removal or installation) so I can't offer you any help as far as properly seating the TC. I always thought it just bolted on to the flywheel and the trans shaft stuck into it like a manual trans shaft would normally stick through the flywheel. Huh, guess I should read up on that before I help my buddy dig into the 99, eh? (I'll start a new thread about that tomorrow -- it's the 99 in my sig)
If it is the 'old' and known-good TC, then it is most likely one of the two issues you mentioned, in which case there are at least a few people on this board a bit more knowledgeable than myself.
'00 Corolla - Daily driver and work-in-progress.
'99 Corolla - On to a better place...