I'm using the Novak Master rebuild so I'm sure our instructions are the same, at least I hope so.
They just say to pull the bearing while the shafts and everything is still in the case.
They reference a "bearing puller" tool in their drawings but it's not something I have had luck finding online.
The tool shown is "amc tool j-25152" also pictured in this link
http://www.toeksplace.com/jeep/amc/6_ManualTransmission.pdf with more detailed information. Looks like they use a similar one on the input shaft bearing as well.
I figured 3 jaws pullers would work but they do not have narrow enough teeth to fit in the snap ring groove...
OK. You forced me to put my thinking cap on, haven't worn it in ages.
Tap out the big shaft from the lower gear cluster and let it fall to the bottom.
Then remove the front bearing retainer housing. The front input shaft and bearing will easily pull out the front of the case by hand, (almost) and all the needles inside the shaft will fall into the bottom. No problem.
Then, with the snap ring still on the rear bearing, support the main gear cluster by hand so it's not hanging on the bearing and tap the main shaft towards the front. The shaft will slowly move forward as the rear bearing is held in place by the snapring against the case. Or, turn the case vertical so the cluster hangs and tap the shaft down from the rear. (Just thought of that now.)
You need to TAP this shaft. Only hard enough to get some movement. Don't pound it hard and do not mark up the end of the shaft. I may have used a drift that was smaller than the shaft diameter so I didn't mark up the splines. No, Wait, now I remember, my shaft was junk, I pounded the snot out of it. Not recomended if you want to save the shaft.
Upon assembly use the Vaseline for the needle bearings as suggested. It holds the bearings in place so good that I did not use any of the recommended dummy shafts to keep them in place. Just go in gently with the cluster, line it up with the housing hole real good, and slide the permanent shaft in place.
Check the splines on the end of the main shaft to see if they are worn. They should be a consistant thickness and tapper the full length.
And when you put the shaft through the lower gear cluster, which is one of the last things to do, use 2 pieces of small rope or nylon strap to lift the lower cluster into position. You can't get your hands in there to do it.