The wires that make up the windings in the rotor are all coated with a varnish or some insulative material, before being wrapped on to the rotor bobbin. This coating/insulation keeps the wire conductor cores from touching each other (shorting out). The coating material is usually translucent, but may have a color tint ranging from clear, yellow, or even brownish, depending on what was selected. The material is put on during wire manufacture and there are many types possible. After wrapping onto the bobbin, and in order to keep the wires in place so they won't rub against each other, wearing off the individual wire insulation, the wrapped assembly is coated or dipped into an epoxy or varnish material that glues all the bits into a solid mass, resistant to vibration and centrifugal force effects. Note: that's resistant, not impervious. Heat and vibration can still take their toll, especially upon minor manufacturing defects that don't show up early in it's service life.
Picture this: Two wires laying side by side in vibration rub along their entire length. Two wires in vibration that cross each other have a single vibration contact area, more likely to wear through quicker than when the contact area is made along the entire length of the wires. In the ideal world, your rotor has all the wires parallel. But, during manufacture, some of the inner windings could be crossed.
Crossed wires that make contact through their insulation, short the electrical path through the device, reducing the amount of wire that electricity must travel through. Thereby, making the overall resistance less than when originally manufactured, so it draws more current that expected from the bike. Compounding on that, since less of teh wire actually has current flowing into it, the magnetic field that it makes is weaker, causing the stator to develop less power for delivery into the bike and/or Battery.
This describes what CAN happen. I don't know that it HAS happened to your rotor. But, since I don't have a specification from Honda about what the rotor is supposed have in the way of resistance, I can only determine if the alternator has full output by measuring the output at various RPMs. It would also be helpful to know the exact load being placed upon the system, if different from stock through "upgrades".
You could also place an ammeter in series with the alternator output (between battery and and rectifier output, and measure its delivery capacity at the RPMs I noted earlier. The Honda Shop manual states it should deliver 6.5A at idle and be capable of 18A at 5000 RPM (when conditions warrant).
The bubbles you found on your rotor could be from dipping the rotor into viscous "varnish", or from the windings overheating and melting the coating. If any of the coating is black or charred, that's a bad sign for rotor integrity.
Awaiting further data...
