Progress!
I manually do the acceleration and decelleration parts by sending pulses to the port. In the middle, I just start the timer and let the hardware do its part so I can do other stuff (like listen to the usart for commands).
Now, I just need a way of counting the number of pulses sent through the port. Remember, the timer is running at 90KHz so an ISR is out of the question. I can manually count the pulses for the acceleration ramps if need be.
Is there a way to rig up a timer to count the pulses on pin 9 (where i'm sending the PWM) and have at least one ISR for every 65535 steps or something similar?
thank you!