If everything fits otherwise, it almost sounds like you're trying to install it crooked and it's binding. Laying under the car, it's sometimes hard to see if it's straight. Or as mentioned, did you use an alignment tool?

I would pull the trans and put it together out of the car, then install the whole thing as one unit. That's what I did and it was cake. But I used a load leveler. Got it from Harbor Freight for about $30. That made all the difference. It would be almost impossible without it. But with it, it was very easy. I can't imagine trying to line it all up and bolt it in while laying under the car. Way more work that way.