Scott,
Bobcad is just cadcam software. It has nothing to do with the performance limitations of your controller. All you can do in Bobcad to affect things is to alter the feedrate. That is not to say that commanding a high feedrate in the program, will result in a high feedrate at the machine. The controller can only do what it can do. So that is where I would be looking to make possible alterations to the controller setup. Again, the whole motor/ amplifier setup has to be capable of what speed that you want it to do.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)