[cncsnw]

Even after running the encoder a bunch I'm still not seeing any errors on the PID screen. I guess that means it's working?

Meaning that if, for example, you start with the count near zero and run it with the drill at ca. 250RPM for one minute, then the count on the PID screen ends up in the vicinity of 2,000,000?

If so, then the question should go to the software staff at Centroid. To the best of my knowledge, the status window actual-RPM display (with P78 = 1) has no multpliers except for varying spindle range (and that would only apply with bit 4 of P36 set).