Fixed the clutch issue last night. Unbolted the bellhousing, dropped the trans about 2 inches and pulled it out about a half an inch. Attached the throwout lever and spring, slid the ball in and then reattached the bellhousing and everything was good to go. Replaced the trans/transfercase crossmember bolts with longer ones so I can attach a skid plate to them in the future.
It has been sitting for almost 2 months without being fired and it started up on the first try after I fixed the clutch issue. The only thing I need to do is re-weld the passenger exhaust to re-attach the muffler. I had to cut it to get it back in position and attached to the manifold.
Just waiting on my driveshafts to come back from the shop and she's trail ready!