So far so good. Screwing around on the Arduino Micro I currently have, I successfully tested a nano-second timer which should be accurate down to about 63 ns. I'm relying on Timer1 in fast PWM mode to run at a pre-scaler of 1; causing each tick to increment with every clock cycle. At 16 mhz that's 62.5 ns. The only downside is that as-written it's limited to counting 4.2 seconds, but that should work fine for this application. Now I just need to work on making it compatible with the odd-ball 12 mhz platforms; otherwise 8 and 16 mhz results in nice round numbers and no chance to accumulate error.
This is borrowing heavily from the code already used for the micro-second timer, only a little simpler and designed to reset the counter at every call of the sub-routine due to the nature of how it's being used and how short it can time for.