Original Author: Bill Williams
My youngest and wrestled for 3-4 hours using a rolling transmission jack. After a long while and not doing anything differently than we had been doing before, it just slipped in - happy - but tired and frustrated. This and aligning a hood are the two main reasons I mate the motor and transmission to the sub-frame before I put them in a car. Mating a transmission really sucks sometimes.
However, if you do mate a transmission to the motor while the motor is in the car: 1. Get the clutch plate and the pilot bearing lined up. The best way is to use an old input shaft from an old transmission, second best is to use one of those plastic tools.
2. Have a strong patient helper.
3. Turn the wheels to get the center link out of the way.
4. Make sure the throw out bearing is oriented correctly. Ears of the throw-out bearing on the release arm, not in the slots.
5. Get the tranmission on a good secure jack, rent a transmission jack, balance on a floor jack, or use an ATV jack.
6. Put the transmission in gear so you can rotate the rear shaft to line that part up.
7. Polish the tip of the transmission input shaft so it will slide easily into the pilot bearing.
8. Do the stud trick to help hold the transmission up while you play with aligning it. The stud trick is to take some bolts that fit the upper mounting holes on the block, cut the heads off, slot them and insert them in the holes. These studs will support, hang the transmission, while you align it. Fix the other bolts, then use a slotted screw driver and back these out and replace the proper bolts.
9. If and only if you think you have it lined up and you can just not push it on, take longer bolts, start them and see if cranking the longer bolts just "pulls" the transmission and the motor together. I had to revert to this one time when the motor and transmission was on the floor. If this works, take the longer bolts out and replace with the proper ones.
You can see the stud trick here.
Bonus points: When installing a transmission: a new pilot bearing, pressure plate, clutch disk, throw-out bearing, resurfaced flywheel, new flywheel bolts or use Loctite on old ones, should be used.
Resurfaced flywheel with step. Mark the timing BB while you are at it.