The inner diameter of the bearings are a tight, toleranced fit onto the spindle. They can be really snug sometimes. The fact that you could "polish" the ID of the bearings and get them on tells me that you prolly just had some kind of debris, or a small burr on the bearings. Those bearing races are pretty hard...1500 grit paper prolly wouldn't do much more than clean the surface, without removing any substantial material.
A bent spindle could make it hard to get the outer bearing fitted with the hub assy on, but it wouldn't effect installing one bearing at a time onto the spindle.
I've had to "tap" a few bearings into place a few times, but it is simply due to the tight tolerance between the ID of the bearing and the spindle surface. I'd say your situation was fairly common. If you saw no indication of damage to the spindles, such as heat(blue/black), or galling, you're prolly ok to go.
Do the hubs/rotors turn easily when installed, with no "binding" in any area?
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