Update i set up timer interrupts to toggle the output pin. and at 100 hz i am getting .6 hz jitter, but at 5k hz i am getting 20hz jitter, so a Lot better at higher frequency. It looks like that is the limit of the arduino, That range will actually work. what i need it for i need less than 2hz at 360hz or less than 32hz at 5kz.
Would a stronger micro controller do better?
Ill post up the code in a little while i am still working on it.