Okay, got back to testing it again, here is what I found
Output 1, does the same thing
If I try and load the output, I can get it to run at higher speeds, if unloaded it pulls out when getting up to max speed
2-4 microsteps make it able to achieve a slightly higher max speed than no stepping, 8 doesn't appear to help at all
the noise is still there, I think it has to do with the acceleration curve and that this is going so fast, I don't remember noticing it during the hello world or other runs, it almost sounds like its coasting (which it is not)
I don't think its broken anymore, I think that's the physics of steppers maybe? I understand the higher current = higher torque, but somehow higher current means less max speed as well.
Also, the reason this came up first of all, everything was working okay, but I was getting terrible resonant noise on the z axis. I tried some things, took it all a part, lubed things up, steel wool on the threaded rod, and that issue went away, but then I noticed the "grinding" at the beginning and end of the cycle (at this point I was just running up and down at max speed to test). I took a part the axis again, tried more alignment things, then thought maybe my motor was bad, as this was the motor I had cut the pulley off of. So I borrowed a motor and ran it out of the system, it wouldn't run with the standard g0 command. I tried my motor as well, it wouldn't either, so I thought my Z axis broke. Unloaded this thing can't run full speed set in the settings, as I just tried, loaded, I can get it to run, so the load of the axis was enough to get it to run properly.
Now that you've had me try a few things, I'm a lot more confident that nothing is wrong. The "grinding" noise still bothers me, but I think its just the acceleration curves and the different whining frequencies of the motor. Did you experience this when running your motors?