1997 Honda Prelude Transmission

Last Night we stayed up until around 6am replacing the transmission and trouble shooting. We had to trouble shoot because now the car will run but only in neutral. Putting the car in any gear, it would either die or act as if it was still in neutral. I'm not sure what it could be. The internals of the transmission looked fine.

Why did it need to be replaced?
A seal was leaking, (I wasn't aware) and all the transmission fluid leaked out in the old one. The transmission got hot and gears started breaking. :( It was so bad that when we moved the car to place on a dolly it was as if something was lodged because it kept catching and we had to force it to roll.
I'm not sure if this could have something to do with it. But that's the story of the old one to help. Thanks!