Alternative to digital rotary encoder

You are correct. I was wrong and flipped things around while doing the RPM & sec/rev units conversions.

I think so -- from an admittedly external, top level control system point of view of a person without any experience with your hardware, the time constant of the plant/system/DeviceUnderTest seems like it would be much much longer than the dt=0.000020s(?) of your control loop.