OK, May sound like a strange question, but do the horn and or turn signals still work right?
Reason being, looking at the schematic, the same ground is used for those three functions; clutch switch, horn, and turn signal relay. If yes, then I would look at the clutch wire between the switch on the bars and the ECU. If you were to take an independent wire running from ground and then ground the pin/tie into the clutch wire at the ecu, you would rule out the wiring and switch both. If it works, the problem is in the wiring or the switch, if it doesn't work, then you're looking at a potential ECU issue.
As far as the fuel gauge, not sure how long the issue has been going on for, but we all know that the system takes a few miles to update after fueling right? Well, I have also seen that sometimes when I have a failed start problem, along with the CEL coming on, I have also had the fuel gauge stay blank for a little while until it "resets" itself. Either way, I would tackle the clutch issue first and see what happens next.
Just popped into my head, but do you have a keyless ignition system added? I'm thinking no since you were riding w/ the clutch switch bypassed for awhile, but thought I'd ask for added info.