8 3/4 pinion shim question

I have a micrometer, but I've just been going off of gear marking compound right now. My main question is which way should I set the pinion (deeper or shallower) because the two bearings are different heights, so when I check depth with one it won't be the same for the other. I don't want to keep trying to press the new one on and off because I don't want to tear it up, but using an old on for measuring won't get me the same numbers.

You're not going to get an accurate measurement doing it that way! No way, no how. The pinion depth is the relationship of the gears to the case, the bearings really should not come in to play in regards to that measurement.

Again, can you see if there is a marking for target depth? Measuring shims with a mic accomplishes nothing if you do not have a final target depth to shoot for.

If your bearings are different heights, then you may not have the correct one for your application. The later 489 cases use a crush sleeve to set preload, there may be a difference in spec between the 489 and 742 case bearings but I am not totally sure on that.