Transmission mounting

Jordan it sounds like you are not getting the very end of the input shaft into the pilot bushing. You must get everything aligned pretty dead straight the get it in all the way.

Hey there Jordan, it is most important that you don't panic - Willys can sense fear in their owners and they love to take a small problem and turn it into a disaster. Like having the input shaft stuck in the pilot bushing so the clutch won't work. Since we all have been where you are there are a bunch of threads in the search engine with good ideas. If you lived in South Texas I would suggest that immediately buy a transmission jack (as I have always wanted to know someone who had one I could borrow). Have fun

Thank you for all the help everyone. I am hoping it just is the angle of the transmission going into the bushing. (I can post a picture soon but it is already into the clutch plate.) would it be a good idea to put a level on the motor, get that leveled completely, then do the same for the transmission ? Also, should I take the bell housing from the engine and mount it to the trans ?

Long story short I've been doing a frame off restoring this cj 2 for my dad as a gift for about 5 months. Almost got the tub back on, just can't do that until this is settled! I am 25 years old and this is my first build, my mechanical knowledge is minimal compared to most people On this forum. I will post build pictures soon.
Thanks ! I will try some of these things tonight and hopefully it wiggles in.

Getting the transmission to line up and slide in is an exercise in patience and persistence. If  you are certain that your clutch/pressure plate/bushing are all lined up properly (you said you used an alignment tool so they should be),  then in my experience, it's a matter of laying on your back, then wiggling and pushing, and pushing and wiggling, often to the point where you are sure that something is not right and then... you hit the sweet spot and it slides in and you wonder what the heck you did, but mostly you are just thankful that you are done.

Is the flywheel pilot bushing new?  If so, the inside diameter of the bushing can compress when driving it into the flywheel...and make it difficult to close that final gap.  There isn't a great way to test this unless you have a spare T-90 input shaft laying around.

Is all part of the fun of owning a Jeep. I would be out there trying to get the gearboxes back in my MB when I was a teen. A few hours out there with the boxes on my stomach as I wrestled with them. Gave it up to go get some sleep.
The next day it slid right in on the first try.
We tell you these things as we have all been through it and learned, something?

Based on your photo, you have the splines lined up on the clutch disc.  This is good...as long as you're certain the disc was centered with the alignment tool...and the disc didn't slip when you tightened the pressure plate bolts.

Okay, so most likely I will need to remove the transmission from its partial spot, and ream the bushing.