I am working on the bike now, and have checked the following things:
I felt around the fusebox for loose relays, they all felt OK, but I pushed them all in to ensure they are seated. Per Jim Moore, I'd like to pull the Cat Code Plug, but don't know where it is.
The resistance between the pins at the coil is .2 Ohms at the input, and 7.25 K Ohms between the post for the spark plug wires. The HES document linked to below says that second reading should be 13K Ohms, almost double what I have. The resistance of the spark plug wires on both sides is 6.2 K Ohms, although I'm not sure what they're supposed to be or if that gives new information.
The battery looks fine, it's giving 12.87V
The spark plugs are both carbon fouled. I've never had plugs look like that before on this bike.
I Without yet removing the alternator belt and pulley, just the cover, I don't see any obvious problems with the HES wire. I did notice that the side of the new belt showed stitching, as if it may have rubbed against the engine breather line, although now there is clearance and I don't know if the stitching always showed
In terms of replacing the HES and/or HES wires, I found this
Is this a good reference?
Similarly for the O2 sensor, no wire damage is obvious
Thank you all for all the help so far!