Never mind, the per-component rotation isn't on the feeder screen, but kept in the pick-file feeder assignment screen, I just missed it there.
With the new motion board and after recalibrating everything, the machine is placing much better than before, did a few hundred 0402 today to test and it's much more precise, and is keeping its calibration. The nozzle Z-height adjustment is still quite off but the nozzle pairs are better matched now.
Also the fiducial recognition has been improved, it can accept more shapes, and you can specify the size of the mark to detect. Although I'm having trouble with it, the threshold settings for one fiducial do not work on the other one... lol