I would actually recommend running X Vertical. The original handibot in the video was a bit lighter (less metal parts and no hood) which made it easier to run at normal speeds with Y vertical.
I'd also recommend turning the speed down in your cut file (edit the bit settings in vcarve and recalculate the cut).
Also the "maximum jerk" settings in the Configuration/Axis menu--these control how quickly the axis ramps up in speed. The default value is 50 (50 inches per second per second per second -- it is the first derivative of acceleration) setting this value to 10 will make the tool much less aggressive when it changes direction and will help prevent stalling.