I know EMC2 with one of the Mesa boards will do PWM out...but I think setup may be a little harder than Mach3.
It may be a LOT easier to buy some step/direction servo drives that will hook right up to Mach3. I think that is by far the most painless way to get into CNC. Steppers always seem to lose steps at the worst time...and the PWM servo drives will only work with custom software or EMC2. Anyway...I think I'm drifting a bit
