Thanks for the thread - please keep posting your progress.

There is an excellent application note on the problem of ramping up/down on:

The ATMEL site: AVR446 'Linear Control of Stepper Motor'

It comes up with a good approximation for linear acceleration without over-taxing the MCU. The simple business of making linear changes to the PWM 'sort of works' but is nothing like the smooth motion one get with MACH3.

Regards Bill Legge