your grasp of electrical seems pretty solid to me. that yellow is suspect . you need to test to see if any of the windings have shorted to ground. I think you may be in the market for a stator ..

 

Winston.....
The wires from the alternator on your bike are a Pink wire, a Yellow wire, and a White wire......
Your white wire was likely stained by color transfer from the neutral switch wire (which is a Green with a Red stripe wire)......
Regardless of apparent colors, your readings of output AC Voltages are within normal parameters for a good stator.....
IF NONE of those first three wires shows continuity to engine case ground (the winding core), your alternator is fine.....

Despite what it reads after charging, ANY 12V battery that reads below 12.0 VDC at any time when just sitting is BAD/damaged/dead.....
Standing voltage should be 12.6 to 12.7 volts after charging and sitting overnight.....NEW does NOT always mean good....
A 1.5 amp charger is EXCESSIVE for use on a 12 ah battery and WILL eventually damage it if it hasn't done so already....
Correct charging rate MUST not exceed 10% of the battery's ah rating.....I recommend a 24 hour charging at 0.5 amps yielding the full 12ah charge....
A "low and slow" charging rate will greatly improve the battery's lifespan.....

The primary suspect in your charging problem is the rectifier.....
Those old Selenium versions (red or orange finned) are notorious for failures, and we usually recommend a modern Silicon replacement.....
Testing is easy: Any/All possible pairs of wires MUST show continuity in only one direction....
Any pair that also shows continuity with the meter probes reversed or shows an open circuit at any time indicates a bad rectifier (bad diode)....

IF you have any doubts, I recommend a modern rectifier/regulator combination which also will eliminate any uncertainty about the original regulator (which can only be tested in use)....
Many here have used the combination unit available from Matt, aka Sonrier, (and a member here) through Sparckmoto with excellent result.......

Any questions: phone me....************....Steve

 

To add to Steve's post, the alternator does not charge the battery at 3000 RPM, it breaks even or a just a little better....The alternator actively charges the battery around 5000 RPM, with max charging around 10000 RPM....Below 3000 RPM, and especially at idle, the battery is supplying the voltage needed to run. Long periods at low RPM cause the battery to be depleted, as you learned.

Also to add, Sonreir, at Sparck Moto has a nice regulator/rectifier combo unit that works very well...Because it has a lower internal resistance then the OEM rectifier, is actually increases the current available a little below 3000. My CB360 breaks even around 2200 RPM, so I am charging better...Sparckmoto's R/R also regulates better so you don't overcharge the battery. Overcharging boils out the electrolyte, also shortening the battery life.

One traverse below 12V on a lead acid battery will shorten the life of the battery a little, but as Steve said, a low, slow charge is the way to get it back to near full capacity. If you look at Amazon.com, they have a Battery Tender Jr, which is 0.85 A max, but is smart, and can be left on the battery whenever you are not riding. Lead Acid batteries last longest when kept at full charge...Other battery chemistry's are different....My CB750 battery is on a Battery Tender whenever the bike is parked. The battery right now is 7 years old, My CB360 battry is 3 years old, still going strong.

Keep the battery charged, and electrolyte level good (only refill with distilled water) and your batteries will last a lot longer than most.

 

Modern regulator rectifier combo unit will greatly improve low speed charging.
I wired Suzuki rectifier directly to alternator outputs and get break even at idle

I can't find the pic of ammeter showing slight charge at idle