jremington:
It may be that the microstepping is skipping steps, which is quite common. Try the experiment suggested by Robin2 with full steps only, then microsteps.In general, microsteps cannot be used for accurate positioning, as clearly explained on this page by an industry expert: Microstepping Myths and Realities | FAULHABER Tutorial
Microstepping usually reduces the resonance, reducing the chances of mis-steps (and
the amount of noise). In a mechanical system with no damping this is especially important.
First sort out the acceleration and speed limits - then experiment with various options
to see if you can increase performance.