I see, what’s the min step size you’re going for?
The current system I am building is mainly optimized around scanning large areas quickly; I have already demonstrated that I can create accurate stitches by moving, stopping, taking photo, repeat, but it's slow (due to the stopping) so I am working on an approach that keeps the stage moving constantly, but triggers a bright flash that freezes intermediate exposures. This gives a good 10X speedup over the simpler model of move/stop/photo/repeat but brings in a number of other challenges.
good luck! are you posting updates anywhere?