I've been keeping a close eye on this thread because my ride is also not delivering as many volts to the battery as I'd like to see. Then again, after all that I've been through with Yamaha, they have yet to come up with a new wiring harness for me (always on back order). Mine will almost certainly be the very last FJR to have the harness replaced (In the meantime I have bypassed a couple of the grounds with 18 gauge wires soldered to the metal spiders and terminated at my fuse block grounds which has a 16 gauge wire back to the battery).
Checking the manual there really isn't much involved in the charging system on the bike - no relays, no switches, just the stator, regulator, main fuse and battery - everything else is fluff, unless there are huge undocumented loads that exceed the machine's capacity.
The stator/rectifier-regulator/Main Fuse/Battery is a direct circuit - power does NOT take a path through the ECU. ABS or any of that other stuff and the likelihood of literally tens of amps of sneak current, even on a very filthy bike is pretty low. I haven't looked, - does the negative circuit use the chassis at any point or is it delivered directly to the battery (I would hope the latter)? If it uses the chassis, then that ought to be bypassed out - it would be poor electrical practise to do that.
Troubleshooting OUGHT to be as simple as following the steps in the manual - checking that the stator can generate adequate AC voltage across the coils (and it should be equal between each leg) and the unloaded DC output of the regulator - from what I've seen it appears that the machine has passed these tests with flying colours - the manual does say 14 volts at the RR output at 5K RPM and that seems to have been exceeded as well.
So it seems that the entire wire harness (well beyond the affected components) has been cleaned up, connectors tightened up and that voltage drop is minimized, though I personally would solder all of those crimped-but-not-soldered connectors in the stator/RR/fuse/battery path - nothing else is implicated in the charging circuit according to the manual. Again, if the yokels have not run a dedicated wire between the regulator negative output and the negative battery terminal I would put one in myself.
It is all very nice that we'd like to officially see 14.2 volts across the battery terminals while the engine is running because that is what the battery people say we should see, but if the manufacturer says that the regulator puts out 14.0 volts THAT isn't going to happen.
So if I read my service manual correctly your bike is within the manufacturer's spec.
The regulator is an industry standard device that has no adjustments to mess up, so you'd think that as long as the stator is delivering at least enough voltage to keep the regulator output fixed at it's maximum it should be enough.
Has the machine let you down and refused to start? Are you just chasing a problem that doesn't actually exist (or, perhaps is it simply that the manufacturer's design is inadequate)?
In any case, the weather is lovely. Make sure your roadside assistance is paid up, then get out and ride the beast. I'll be out riding in Vermont today.
