They have a 'diagnostic system' for the FJR? I see no reference to one in the service manual.Actually, it does NOT exhibit the symptoms that the recall was designed to deal with - your symptoms are related to a different connector.
The real problem is that the recall was half-a**ed and doesn't resolve all of the potential problems - in fact, I believe I already mentioned that it can exacerbate the problems with other spiders because of increased current flow ttrough the one they tried to fix.
I suspect that even if they did the 'install only a jumper' recall because the S4 wasn't far enough gone to replace the harness, it might continue to deteriorate - however your symptoms point to S6 and S7 (or perhaps one of the 2 undecoded ones).
I'd open her up and take a look. It takes a half hour.
Well, I just spoke to the Service Dept. at Stadium Yamaha, they were very helpful, by the way. He indicated that they've done "hundreds" of the recalls and that they've never had to replace the entire harness because none of them were "that far gone". He said that he'd need to put the bike on their diagnostic system and see if they couldn't find the trouble. The problem is that they're 2 weeks before I can get the bike in. Crap.
He also indicated that it could be the ECU.
Whatever, I'm not very good at this part, but I guess I'll try and find the damned "spiders" myself and start checking them out.
I would start by saying that based on the issues you report there is no way that it can be the ECU - the machine is old school as far as the impacted parts of the electrical system is concerned.
When the issue was simply a personal crusade I had calculated that rate of total failure for FJRs in the affected series appeared seemed to have been around 15% at the time (based on the number of failures reported in the original thread on the FJRF009 topic) . . . the key may be in the phrase you quoted; 'that far gone'. I suppose they could have let some marginal units out the door and it might come back to bite them.
But, based on the symptoms you reported I am confident it will prove not to have been the only Spider that Yamaha looks at (S4), but rather that one of the others has burned up. If I'm right it will be interesting to see whether Yamaha steps up or whether you get a bill for the service.