Align engine to transmission on install.
 

Okay so I'm basically like 90% done swapping the engine out of my 97 cherokee only thing is I can't get the transmission and engine to line up. Any suggestions? How do I get this all to mate up?

Don't force it, it will go easy when it goes. Sometimes taking a break helps.

On a chevy it's important to make sure the torque converter if in all the way "home" IIRC. Close attention to the gap between the bell-housing and the engine can help you check you have the angle correct. I've never used an actual tranny Jack, that might hold it at the wrong angle, just one of those small floor jacks and a block. With that you can tip it this way and that and feel whats going on. If you can start a bolt, fine, but don't crank it in and force it, it will go easy when it's lined up right.

Slow slow slow. Take your time might have to jack the transmission up a little on the bell housing to make it level. Also go SLOW