If you have an automotive friend you trust, or better yet a biker friend that does his (or her) own work, get another set of eyes on your wiring connections. I have attempted to follow the various threads on your charging problem and I'm personally not convinced changing your alternator will fix your problem. The two things your testing with a meter will not tell you:
If you have a low resistance connection with the meter, it can be one strand of a dozen that show those results, but will not pass enough electrons other than to indicate on the meter. VOLTAGE DROP
The meter is measuring many turns of wire designed to develop a magnetic field, so a low reading is "good" but cannot tell you about the magnetic field. AMPERE TURNS
If I were there, I'd be looking for defective electrical connections that won't show with a meter. Like a 12 automotive test light, some medium duty wires to jumper around suspected connections.....you need another set of eyes that understands the electrical portion. Your measurements, (if I followed all of it correctly) indicates that you should have a charging alternator...but you don't.
Yes, there's the possibility it may not be turning, but only having been a member here for about 4 years and having the smaller alternator as you do, I don't recall having ever seen a posting for one that didn't turn.
I'm guessing, it's in the manner of your testing that would be allowing you to miss something that could be narrowed down by some more unconventional methods.
Most people on here have had that "loose battery connection" sometime in your life that allows the courtesy light to go on in a vehicle, but won't crank the starter. That's the closest analogy I can pass along, but there are many more connections here and more difficult to follow with Honda's wiring diagram.
Moral support at this distance only, but I'd get an "experienced spark chaser's" eyes and brain in with you. If it were me, I'd be jumpering power and ground leads with wire, a 12 volt test light and powering that rotor from the battery just long enough to see if it charges (two seconds or less).
Please re-inspect your wire connecting points for any metal that isn't clean, shiny, and looking like new and pull lightly on wire connecting points as it may show a breaking of all but one or two strands of wire that would still test as good. Any wire insulation that appears melted is also suspect.