When it rains it pours..

[zman]

I have never looked at the schematics of a 1000 but I think I will later, If it runs parallel to the ignition but it not a direct link to the ignition you could remove them and start the bike.
If they have been bypassed you could start the bike.
If the harness or any wiring modifications allowed it it could draw its power from another direction.
I understand your question I just am not familiar with the wiring of the GL.
There must be a good reason if they are part of the "ignition troubleshooting" procedure.

 

[Ansimp]

If you pull the diode out power still follows the yellow path to the starter solenoid and power is still provided by the red path to the coils as per the run circuit. If you view the photos in my gallery you will read a written a description of each circuit. :yes:

 

[slabghost]

Wire both coil feed and dyna feed through a relay. Activate the relay with a toggle switch. that will eliminate all of the stock wiring. If it runs right then. All you have to do is check every wire in the stock ignition circuit and all the connectors.