You can do the whole thing with PWM. In my project of making VGA output I needed both vertical and horizontal sync pulses. It sounds similar to what you are doing. You need the pulses a certain width apart, and with a short pulse time. Project page:
Example screenshot:
In that case I had a 4 uS pulse with a 32 uS period. Those figures can be changed by the timer configuration values. This doesn't rely on ISRs at all (for the pulses) since the timer does that.