Well I can help with the chatter. Raise the acrylic up, all the way. Top out the spindle and shim up the bed until it moves the work piece all the way up. Put some 2×4’s or something underneath it. Then if you are still having issues try a single flute bit, then you literally only need to move half as fast as a 2 flute. If you still have an issue try a single down flute…my fav. If you keep a vacuum on it or compressed air it will keep it cooler if you really need it. You should also get rid of the vacuum straight piece and just mount the hose. That straight rigid piece pulls on the cutter, a lot, like a breaker bar. There are tons of little things that can be done. CNC machinists get payed very well for a reason.
As for your movements, it is hard to say. I would guess a bad connection, but you say they are good. Next would be the drivers but I have zero experience with external drivers, I would say check for signal noise. Maybe end stop issues or a power wire crossing your driver input. You might need to isolate your wires more, or use shielded, or maybe they got cut on the conduit edge somewhere?