Got everything back together and up and running again!
Replacing the belts was fairly straight-forward. It's clear they didn't design this with easy belt replacement in mind, but it wasn't too bad. The most annoying part is getting a good tension on the belts. There's no jack screw or other provision for tension adjustment, you just shove the motor back in the slots and tighten it down. That leaves a lot to be desired...
Spindle orientation was pretty easy once I got the correct instructions. Here are the instructions for that (Yaskawa drive) in case anyone runs into this issue:
1. Calibrate machine axis and tool changer.
2. Set P2-02 Market Offset 1 on the A1000 inverter = 0 first.
3. From the Manual screen, press the “Orient Spindle” softkey, and then Cycle Start to orient the spindle.
4. After the spindle is oriented, press the “Spindle Off” button.
5. Turn the spindle in CW direction a minimum of two revolutions and stop it at the actual orient position (I marked this before removing the belts, which really helped!).
6. Monitor U7-02 Dist From Marker on the A1000 inverter to view the current orientation encoder counts.
7. Set parameter P2-02 on the A1000 Inverter (0~4095) as viewed in U7-02 to adjust orient position and then escape to Dataset.
8. FOR 10K SPINDLE NON 1:1 Ratio ONLY F1: Set N95:214 to 1, force rotation before orientation. (not necessary for me)
9. Turn on the spindle CW or CCW in manual mode and perform the orientation several times to check the orient position.
Overall this took me a couple hours, but when I have to do it again it should go much faster, plus I bought extra belts for when the time comes.