You didn't mention what stepper motor drives you're using, but almost all require a pulse width of at least 2 and some work better with it set to 5 or more.
A steady clicking noise like you're seeing can often be caused by a process running in Windows. But, they can be very hard to track down.
I've never used a mill, but I'd say that 200 velocity and 30 accel are quite a bit higher than most users are running? Especially with 425oz motors, which are about the slowest sinning Nema 23 motors you can get, unless you are running them at 72V. I'd try cutting both of them in half and see if you get better results.