I would like to add that you shouldn't use the Arduino platform if you want your MCU to handle timings smaller than the crude level of 1ms. The current models (maybe DUE is different, but I haven't used it) can't really handle processes with very fine time resolution.
This is due to the high level of programming, which given the 5MHz clock can't use the hardware effectively enough.
This is due to the high level of programming, which given the 5MHz clock can't use the hardware effectively enough.