Electrical issues - Alternator? Rectifier?

[Fazerider]

... Are those values that that other post mentions (90v!) correct? If I disconnected the plug from the stator to the rectifier and measured that, without load, rather than the input to the RR, would I get them then?

Yes. That webpage has me slightly puzzled, it states that the AC voltages should be that high on-load which is possible with certain methods of regulation, but not the one that they show as being used by the FZ6.
Shunt regulation simply loads the magneto heavily when the battery voltage gets to the 14.5v region so the AC voltage shouldn't be anywhere near the figures quoted.
Off load, i.e. with the white leads not connected to the R/R, the voltages will increase pretty much in line with engine revs. If you try that measurement I'd keep the revs below 5000rpm as I'm not sure what the insulation is rated at… and be careful, the voltages are potentially lethal since they're coming from a low impedance source.
I still feel that a cheap aftermarket or second-hand regulator/rectifier is the simplest way to diagnose the problem.