Having a devil of a time getting transmission back into truck. Have made 2 attempts with the same results. Get it to the point where I have about 2in left to go and it just stops. Have installed/removed clutch twice, each time with the clutch tool. Checked clutch disc to actually see if it fit on input shaft and it does. Even made some long dowels/studs to screw into block to align the transmission up and still no go. Feel like I am overlooking something simple. Also tried tilting the motor back as much as I could. One thing I do notice is the exhaust crossover pipe heat shield touchs the top of the bell housing. Anybody had any problems with the crossover pipe getting in the way?
Clutch kit & flywheel is from marlin crawler.

 

The crossover is close, but it shouldn't touch. I went through a similar experience years ago when I did the clutch in my 93. I fought it for over 2 hours and could just not get it to go. Finally I gave up for the day, had dinner and went to bed. The next morning I tried again and it popped right in... to this day I don't know what I did different to get it to line up.
Since you used the clutch tool it should go, just have to find that magic angle. When I did my engine swap, I seemed to have a little more luck with the bell housing held up high close to it's operating position, but I was installing the engine. Transmission was still bolted in.

 

Finally got it seated this morning and everything all buttoned back up. Have to wait for battery to charge before I can test her out. She has been sitting a long long time.

Guess I was just a tad off on spline alignment, threw the shifter in temporarily, put it in 1st (had it neutral) and with a little rotation it slid right in.