I do not believe you thinking about this correctly. The bearing and its cage should be the same dimensions or it is NOT RIGHT, part numbers the same or not. Did you install the new races all the way in? Sometimes they can be tricky to seat all the way. It pays to have a good driver set to make sure they are not cocked and sit all the way against the machined surface.
Also, bearings do not shrink,compress or 'wear in' over time, or at least they should not. Sometimes I give the pinion a couple short whacks to seat it properly but that has nothing to do with setting pinion depth, only tightening the pinion nut when setting preload. Again, when pinion bearings wear, the rollers get scuffed up. The cage does not weaken or compress unless there is a catastrophic failure. Usually what happens is that a pinion seal leaks and the fluid gets low, uncovering part of the bearing. You can guess the rest.
Also, there is no 'wear in' type of thing going on here. You probably don't want to tow a trailer with a bulldozer on it right after you do a rear end but generally there is no 'time' consideration, only surface imperfections that can cause noise or some other mechanical failure. Pinion bearing preload and backlash are the measurements that compensate for differences in machining tolerance and driveline shock. Gear oil is the cushion between the surfaces. If you were compensating for 'wear in' then you would keep having to re shim the thing every time it shifted a little.
The pinion depth is either correct as evidenced by the checking compound or its not. If it's not, it will have to be taken apart and shimmed accordingly, either towards or away from the center line. You will have to determine how perfect you want to make it. If it's out either way, it will probably be noisy. There are shim kits available from all the major driveline vendors that have more finite variations than what came in your kit.
And again, even if you have a dial indicator and stand, where is your reference point in regards to the case? You need to find the exact centerline before you can make any type of determination on whether the pinion should move in or out. I don't know, maybe you can make it work like you are describing, but I do not believe it can be done without a lot of trial and error.
When I have done them at work, generally the only things that get changed are the bearings, (like you are trying to do) and we always reuse the shims so we don't have to measure for pinion depth. Sometimes I even reuse the crush sleeve so I don't have to kill myself trying to set pinion bearing preload. I can say for sure that I have NEVER seen a replacement bearing that did not match exactly the one I was replacing. I have had the experience where I installed one that 'looked' correct but ultimately was not. I kept trying to make it work thinking it was right but it was different just enough to throw everything off. I had to taske the whole thing apart and re-do it. Not fun!
But hey, I could be wrong on all of this or possibly misunderstanding what you are trying to accomplish. Please, don't get me wrong, I'm not an expert at all. I think though, that your have some misconceptions on some key elements of setting up a diff. Mainly though, you need the correct tools to do the job right or you are just guessing. I hope you can make it work without the tools but you would not be asking the same type of questions if you had them, it would be evident.
Sorry for the tone, just trying to help steer you in the right direction. It's not an easy thing to do, I've screwed a few up and it's not pretty. The tools will make it easier to 'see' what is going on.
