Reinstalling the transmission with its long top shaft can be a little intimidating if you haven't done it before. I hope this little article takes the intimidation out and makes it easier.
First, make 3 alignment dowels. 1/2 - 13 by 10" by cutting the heads off regular bolts. do not install a dowel in the hole that corresponds to the steering post mount, as that will interfere.
put a little lube on the pilot area of the shaft prior to installation.
if you have not depressed the clutch when the tractor was split, then the disc will still be aligned properly. do not depress it during re installation of the transmission.
if you replaced the clutch as part of this project, you should have used an alignment tool on the disc, or a old top shaft, or centered the disc in the pressure plate (least effective, but will work).
slide the transmission shaft into the torque tube. the first thing you will hit is the clutch fingers. remember, gravity will make the shaft typically hit the bottom of the holes you are aiming at.
the transmission will now be on your alignment dowels. slide it in to where the spline on the shaft hits the clutch disc spline. check the gaps all around the transmission to see that you are square with the torque tube. put the PTO in gear, trans in neutral, and rotate the PTO shaft to align the spline. You should feel the spline bumping the clutch disc as you rotate it. some shaking of the transmission may be needed to as you push the transmission forward.
the last, and generally most difficult to align, is the pilot bushing. It is located in the end of the crankshaft. you will know you are at this point when there is about an inch gap left. Check your gaps and shake and rock the transmission somewhat. it should pop into place! If not, take a break, check your alignment, and go again. It will work! There is no partway here, it is either in or not started.
As a last resort, have someone depress the clutch while you rotate the PTO shaft and push forward. The taper on the end of the shaft should walk up into the pilot bushing.
Remember: you must have the tractor properly blocked and on a splitting stand of some sort for safety. I cannot stress this enough, because you may need to get a little physical shaking the transmission. Additionally, it is much easier to install if you suspend the transmission with straps as shown. The give of the straps, and the ability to move the transmission up and down independant of the torque tube is very important
use bolts to 'pull' the transmission into place until you have engaged the permanent alignment pins. That last 1/4 inch gap means that you are successfully engaged in the pilot. you cannot force it to go if you are still at the 1 inch point. The shaft fit when you removed it, and even if you replaced the top shaft, the pilot bushing has been in that crankshaft for 50 plus years, and is worn a little larger than the new shaft.