Dana 60 - Pinion depth problem
Wow, a total change of over .100 should be something you can see.
I would start by assembling each bearing set (old & new) side by side on a flat surface, pinion side down.
They should be close, even if the old one is worn - as long as it has a full set of rollers.
Can you swing by the bearing house & measure a second bearing? Take the new bearing with you and compare it perhaps?
It looks like you have covered all the basics already. I have had a bad (or wrong) bearing drive me nuts before.
Good luck
B.