Forman, delighted you're back on the project...The current assembly stage can be confusing.
From my experience, if the transfer case has never been rebuilt, and the shaft has the correct factory shim stack, you can simply clean and reuse the original shims with the new bearing set. Tolerances on bearings are so close with quality bearings that you will be simply "restoring" the original end play when using the factory shim thicknesses with the new bearing set.
In case the unit has been rebuilt before, and if you did not check end-plays before disassembly, you might want to do a "dry assembly run" trial fit using an old bearing cone (assuming it has little tolerance wear!) with no seal in place. Once you're confident that you meet the end play I talk about later in the book's steps, you can replace the used outer output bearing cone with the new one, installed with the correct shim stack in place behind the bearing cone. During final assembly, install the seal before placing the U-joint yoke onto the shaft as described in the book. The yoke will pull the new bearing cone into position on the output shaft.
Note: The rear output bearing cones "sandwich" the retainer's bearing cups. The shims set the shaft endplay by spacing the distance between these two output bearing cones. When you place the yoke on the shaft and tighten the nut, you compress these parts and can then read the actual shaft end play between the bearing cones and the cups. Shims determine this spacing. You can even do a trial fit of the output bearing shims using just the bare output shaft and the retainer held in a soft-jaw vise.
Shaft shoulders seldom wear, so these tolerances should be right on when using the same case, end housings or retainer plates, shims and properly fitted clean parts. For trial fitting, I make dummy bearings from the old bearing(s) by sizing the I.D. of the old bearings with a drum sanding arbor disk or burr grinder, making the bearing a light finger-press fit over the shaft. (Size the bore uniformly.)
This will make the trial fit of the shims much easier. You can slide the bearings on and off the output shaft without needing to drive the shaft through the outer bearing cone or use a puller or press to remove the inner bearing from the shaft. The inner output shaft bearing (new one) can be pressed in place on the shaft at any time, as the shims fit between the two bearing cones. For trial fitting, you can even create just one trial fit bearing—the outer one. You can perform trial fitting for end play without the seal in place.
Note: The rear output shaft shims go between the two bearing cones, inboard of the outer bearing cone. To see the relationship of shims and end cap/bearing retainers, you'll find this parts schematic diagram helpful (courtesy of 4WD Hardware):
Forman, here's an example of my dummy bearing approach and how to create dummy bearings: http://www.4wdmechan...er-Service.html. See steps 65-67 in the article. What you will discover is that old bearings without excess wear have very close tolerances to a new bearing. Obviously, if the bearing is damaged or excessively worn, this will not be true.
Once you know that endplay is correct, you can place the rear output shim stack on the shaft between the two bearing cones, inboard of the outer bearing. Place the new outer bearing in position against its bearing cone (inboard of the seal). The bearing cone tapers should face toward each other. Install the seal in the output housing as described. The seal captures the outer bearing.
Protect the seal from damage as you slide the end housing, outer bearing and seal over the output shaft. Use the U-joint yoke to pull the outer bearing cone into position on the shaft. Once the cone is seated, you should have the correct shaft endplay—verify it.
Trust this helps, keep us posted!