Poking around in the service manual for my PC800, I found a section talking about the ignition system. The ignition pulse generators (page 16-2, item #4) and associated wheel are just what I need to measure in order to time injection events. I hope that I can read them with a MegaSquirt without interfering with the stock ignition system. Perhaps after I get the bike well-tuned, I will dabble in ignition control.
The front pulse generator runs on the white/blue and blue wires while the rear pulse generator runs on the white/yellow and yellow wires.
Page 16-8 in my manual gives a good schematic view of the pulse generators and their location.
I believe these are also called crank position sensors. They are most likely inductive in nature, giving a voltage spike with every passing tooth. The PC seems to have seven teeth with one area in between teeth having less metal than the other areas. This most likely will lead to a lower voltage in that area. That will show me where top dead center (most likely) is for the engine.
It looks like the NT700 uses the same technology, although much more advanced, to generate timing data.