Wow, Great PDF. Your Amazing Glider.
Softail,
So looking at Page 4 Figure 4, I assume this is the setup you are using. If you are, there are lots of things to check. Notice the #9 Rotor. It does not state that the windows cut into the rotor are used for an Infra-red chop or ferros metal density (reluctor) identification but I would take a look and clean whatever method they use. If Photo beam method is used, crankcase oil vapors coming in contact with photo beam path would be a killer.
Questions I have:
1) Does page 4, Figure 4, resemble what you have installed on your bike.
2) Are you using the "Green" wire (Vacuum Switch for improved economy) or is it taped off.
3) Which coil are you using (can be single stock <4 ohms, or Crane 8-3006, or 8-3005 or Duals etc)
4) I assume you are using the brown wire for your electronic tach. At ANY time does your tach get erratic, jumpy, when engine starts to back fire?
5) Did bike just start breaking up like this on its own or was some change or modification made at the time this started happening.
6) Do you have access to a Good timing light.
7) Remove the access cover to the HI-4. What position are the dials in for MODE & ADVANCE SLOPE.
Hoop!