A couple of random thoughts from the peanut gallery:
This is the first bike I've had with CC and I really haven't ridden it all that much, but I find that when I want to slow down that it's instinctive to roll the throttle forward. I guess I found that feature by accident because I don't think I'd gotten an owners manual yet when I started doing it. I don't think I'd bypass it.
Since we have at least one bike with broken wires here, has anyone done a resistance check on that switch? It's in series with the others but feeds the main ECU rather than the brake relay and ABS ECU. This is the CC circuit, and is normally powered where the other one (BLC) is normally open.
The only thing I can find that's electrical in the transmission, is the neutral switch and it doesn't interconnect with either ECU or the CC circuit. As I recall, the gear indication is a calculated value. If shifting without the clutch shuts down the CC, I think it must be because of a momentary difference in wheel speed. Edit: There actually could be many software related flags that would turn off the system in that circumstance.
Part number changes typically happen for one of three reasons. They made a change in production techniques; there's a change in manufacturer: both of those are driven by the supply chain; or because a part was deficient. The last one is generally driven from the field. A quick search yesterday seemed to indicate that the clutch and both brake switches are unique to this bike. If there was a deficiency in the part, it seems it would have had to have been found via internal testing by Yamaha, because almost all Tenere' problems are going to show up here pretty quickly. Apparently there has only been some minor issues surrounding the foot switch to date. I would think that the engineers would be all over Sigeye's switches if they had found a problem with internal testing. The other reasons for part number changes could still be significant. I'd like to be able to compare them side by side.
I'm curious how Sigeye's switches would test using mebgardner's technique and if any of them have resistance across them like gv550 found. Were Sigeye's new switches the same part number as the originals? Are the old switches still around?
It's interesting that Sigeye had the relay chatter and if I understood correctly, solved it with a new relay. With a new part number for the relay too, I'm wondering if the new coil may stay closed with a little less current. The circuit that opens the relay, forks before going through the relay so neither ECU is dependent on anything that goes through the relay. That's why I tend to believe that the chatter was symptomatic rather than a cause of these problems. Of course there could be multiple problems between the affected bikes. It would seem unlikely, but certainly not impossible.
It is still possible that this problem is software/ECU related. If that's the case, we are unlikely to find it and will be dependent on Yamaha to do so. I'm still betting on the safety circuit(s).