Letting everyone know on the progress since the last time I wrote here.
I got the new rectifier. The voltage on/current to the battery numbers improved, of course, but not quite to the level i'd like them to.
I didn't do a full-on test of current and voltage at all rpm's at with low and high beams, but with the low beams, the bike starts charging the battery at around 2000 rpms, and of course at even higher ones if the break light is on. So, since the bike is my everyday commute, this is not acceptable.
I started by assuming that the alternator is ok (the resistances on the three yellow wires). Next up was the field coil - I tested it by measuring the resistance between the connections on the Vreg - white/black (+ terminal of the battery) showed 4.8 Ohms, white/green (ground) showed 4.3Ohms. If I'm not mistaken, the these numbers should be within 10% of 4.8 Ohms, which they roughly are.
Next up was making sure that the Vreg is getting the right voltage on the battery. This is where it gets interesting.
First, with a battery disconnected, but the key on, I measured the resistance between the green wire and the battery minus and got 0.7Ohm. Then, the resistance between the black wire and the battery plus terminal - same result. Given the "embedded" resistance of 0.3Ohm of my multimeter, these values are quite good and should not cause a voltage drop given the wire isn't load-bearing.
Next, I connected the battery, key on, and measured the voltage on the Vreg - it was 11.6V vs 12.7V on the battery! So, one volt was lost on the way, and I need to figure out where. I found this wiring diagram for the CB550, and marked the connections I need to examine. The diagram is attached.
I took out the whole electrical board with the Vreg, rectifier and flasher, etc, and brought it home. I will write an update here within the next couple of days to report on the progress.