You'll have to remember, I know how the electrical is supposed to work. But, I don't have intimate knowledge about the physical arrangement on your bike.
I don't have a 650, only admired them from afar.
Therefore, I don't know if the female connectors you refer to, belong to the alternator or R/R side of the connection between them. The Clymer wire diagram gives me no such information.
It is too soon to worry about a 2.2M ohm or 1.9M ohm measurement of the R/R. Because of the way an electronic R/R works, measuring the R/R with a simple resistance measuring device requires more skill and technique. Further, since I don't have abase numbers to compare from a known good one, and don't have and internal schematic of the device. All the numbers you've given so far say is that it is NOT definately bad, or a sure source of a charging problem.
The rotor, on the other hand, has reported numbers that are a clear indication of a problem.
Turning the crank for a rotor reading...
As a vereification of a former measurement, I'd do both. Bump it with the wheel to see if you simply have a bad spot on the slip rings. And, then run it to see what it reads in an operational state. It is possible, that running it may get enough friction to scrape through the glaze. If you do run the bike to measure the rotor, completely disconnect the R/R from the bike for the test, as a precaution to save it from further damage.
But, honestly, if it were my bike, and I measured a reading such as you reported, I would dismantle enough to physically lay hands (and probes) on the brushes and slip rings.
My unfamiliarity with your specific machine configuration prevents my detailed alternator access procedure. Perhaps other forum members can provide info, if Clymer is unavailable. I can only direct WHAT must be done.
I haven't looked. Aren't there Honda Shop manuals for your bike available in the manuals FAQ? I'd rather have that than the Clymer, anyway.
Cheers,