This group may not be the right place to ask, since all of your problems seem to relate to the controller? I use Mach3, and the limits in that are controlled in the setup of Mach3, so I would expect you have a setting in the 501 which needs changing. *I* certainly work with the top surface as '0' and machine down below that, so VCarve is working correctly
Spindle speed is very much a problem for the controller. The first thing I would be looking for is what connection is giving a speed pulse back from the spindle. Probably a question that only your supplier can answer quickly.
Machining speeds can be a bit of black art, and depend on the actual cutters you are using. The data on the cutters will provide some information on cutting speeds, but the first selection is material ... I would not expect to be using a cutter designed for ply in steel.