When I ordered my clutch from Peter I had him send a resurfaced fly wheel too, since I didn't know if I could find a local shop that could do it to his specs, and I didn't want to wait.
Before I pull the shifter on any transmission I put the transmission in gear so I can rotate the output shaft to align the input shaft to the clutch splines.
The 5600 was the heaviest gear box I've ever dropped out of a truck, and it was the easiest to stab back in. I was laying on my back, in a cold garage last Oct. Yes I was praying, and using a real transmission jack.
One other thing, when the transmission starts going back in, go slow. Look at the mating surfaces of the bellhousing and engine, and keep them parallel, side to side and up and down. I hope that makes sense.
When the transmission won't slide in any more, turn the output shaft while GENTLY pushing the transmission in. When it slides in, you'll know it. Then get back to watching the mating surfaces of the bellhousing and engine, and keep them parallel, side to side and up and down. Don't forget you can jack the engine up and down too, to change the angles. Just go slow, it'll go in.