So I don’t know if anyone is still on this thread, but I think I have isolated the problem. I have had the problem on both the Y and the Z axis. on the the axis I messed with the driver voltage and that fixed it. for the Y I have no idea. the problem is that the feed rate is clearly messed up, though it does not say so in the firmware. it moves twice as far as the x axis with each step on manual control, and has this terrible screeching sound as it does so. I have switched motors, and when I switched x and y axis, the same problem was happening with my x axis. I would love help with this last issue, and then I would be eternally grateful, though I get that this is very boring and not worth most peoples time.