Could it be that the box was set up wrong to begin with and thats why the bearings were notchy when I got it?
Seems plausible since deep groove ball bearings have a limited lateral load rating versus the radial load they're designed to take at a given speed. The bearings would work but their life would be reduced from design life = early failure.
Fig said, " it was all pretty repeatable within a few thousandths."
Wow, your measuring method must be repeatable down to at least one thousandth, or you will have problems. You need to shim it to within .002" of your target.
We found that many came from the factory with too much end play.
Don't ever assume that anything from the factory is correct. We once found an extra part in a transmission just flopping around and it jammed up the gears. Brand new bike too. I could write a book on factory errors. Oh, yes, I did and it is on my website.
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Last night I reheating the bearing pockets in the case and reseated the shafts with a plastic hammer. After measuring for the fiftieth time I got better measurements for the input and output shafts. Lay shaft didn't really change. I've made piece with where I'm at now, shims have been selected for each shaft. Tonight I plan on closing her up.
With the experience I have up to this point It seems this measuring bit is more art than science. if you add up the differences in variation you come across while measuring each component you realize that coming up with a gap of two thousandth of an inch is kind of a guess in the end.
Thanks for your help, I'll let you know how it goes after I close it up.
Fig, your frustrating experience is exactly why you need to measure and remeasure.
I've only done one tranny and found I had to measure lots of times as well.
Also making things more difficult is measuring variations in one pocket etc that are greater than the specd tolerance.
Shoot for tight, and judge success by the ease of turning the input shaft. If you're confident that your measures are close, and you find the input shaft tightening as you button up the rear cover, give the input shaft a whack with the plastic mallet. You'll most likely find that the shaft frees up.
Hitting the end of the input shaft with a mallet will 'bend' the cover rearwards, creating more endplay. It is an effective method.
Well finally got around to closing up my case.. was on vacation, plus my hobbies get lowest priority.
Anyway I actually put the cover on and took it off again three times. Each time cause the output shaft was too tight. The first time it wouldn't turn at all after torquing the cover. After reducing the shims several times it now turns but it feels firmish. In the 5speed repair video I have from Cycle Works it's shown that after closing up and torquing the cover the output shaft turns nicely and the output shaft shim can be moved around with a pocket knife. My shim won't slide around in the pocket like shown in the vid. The shaft turns tho just feels ever so slightly firm. Question is what's too firm, will things loosen up when it's back on the road?
I would try heating it up in the oven and allowing it to cool down again. Check it hot and then when it cools down.
If you live in a place that freezes and will ride in that cold weather, then you need to have it "free" at that ambient temp.
Were you trying to put the depth mic on the inside race? You must measure to the outside race, as that is valid. The inner race flops around and gravity allows it to show that it is deeper than reality.
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I'll try throwing it in the oven like you suggested maybe things will feel better after a heat cycle. By the way the input shaft was slightly stiff too until I hit it with a plastic hammer like Me109 suggested, then it was fine. Hitting the output shaft didn't change things however.