Q: Ford explorer 1994 4wd manual: gap between transmission and drive shaft case after removing trans

Hello, so I recently removed the transmission from my explorer in order to replace the clutch master. I got it off fine, though in the process I ended up having to detach the high gears from the main part of the transmission, which is part of my problem now. I replaced the clutch ring, and greased it well, then realligned the transmission and got it back on, all without disturbing the plates. Then came the problems, I have about a 1 inch gap between the transmission and the higher gears section of the trans, and then after that, I have about a 2 inch gap between the 4wd drive shaft case and the trans. I think the gap between the higher gears and the rest of the transmission would close up fine if I could get that drive shaft case tight, as I made sure everything lined up inside, but for the life of me I can't get the differential back on. Any help would be appreciated, I'd rather do the work myself if possible instead of getting a tow truck, but am willing to take it in if needed.

My car has 50000 miles.
My car has a manual transmission.