Recently I installed a new transmission, but one side is not resting on the mount. There is about an inch of space straight up. It’s a gl-10 with an ej22 that has fresh mounts and a 93 pushbutton trans that also has fresh mounts. And the trans is fully bolted onto the engine. I can’t figure out why it’s just not falling into place.

Have you got the correct gearbox bracket fitted?  There's a left and a right hand bracket.  Get them mixed up either side or have two the same and things won't line up from memory.

 

Cheers

Bennie

Picture or explain better?

 

Support the engine and transmission weight so you can then twist it around and line up the engine mount holes in the crossmember.

 

Try unbolting the rear trans mounts from the back of the underbody to give more wiggle room.