If you want to be able to control ignition advance/retard, just move the pickup X degrees advanced, say 10 just to pick an arbitrary number. So by placing the pickup 10 degrees advanced, you have X milliseconds to process timing for THIS ignition cycle instead of being 180 out.
You wont be running more than 5000 rpm I'm sure so timing of the Arduino shouldn't be a problem with a single cylinder ignition setup.
One caveat that most should know, spark control is risky without also being able to control fuel.
Ed