Looks like your moving along on the RT project. I like the idea of closing the loop with stepper motors.
I did play with an Arduino Uno and Due, to see how fast I could count an encoder, using edge triggered interrupts. I have a 5000 count unit, that I drove with a electric drill. The Due could keep track of counts with 9 microseconds between pulses. At least that is my memory. I was loosing pulses with the Uno. The drill was in low gear with 350RPM max, and full throttle was too fast.
This experiment is for the project I need to get back to, which is putting an encoder on a milling machine power feed, which has a universal motor. The speed controller in it is based on an SCR type circuit, as AC power is fed to the motor. I would change this to DC and PWM drive it. There is no feedback to maintain constant speed, but the goal is to dial in a feed rate base on spindle RPM. Also I want to add electronic travel limit.

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