As for my tolerance setting I believe it is at .01 in. Should it be any lower?
If you're working in mm's, try .02 or .03
How large is the model?
What is your stepover?
Id it the roughing, or finishing that takes so long?
What kind of processor is in your PC?
The printer ports are on the Smoothstepper. But they aren't the same as real printer ports. Mach3 sends the commands to the Smoothstepper via ethernet, and the Smoothstepper sends the signals out of it's "printer ports". The reason you can't use Mach3 on a 64bit OS with printer ports is that the printer port driver won't work. The SS doesn't need the printer port driver, because the PC isn't using a printer port.