I think adding the ability to reset a given stage could fix the misalignment bug, as if it just sets the stage to a given state, then problem solved, hopefully. (seeing as undoing does nothing)
that or make it so the visuals are overlapping a series of boxes, so while the visuals fall appart, the hitboxes dont.
ok, so a reset button wont work. but locking it to the grid shouldn't be that hard. (also for some reason the first button segment has like 10 FPS, and the desync seems to happen when in the middle of moving the FPS changs to much.)