I'm missing it. Where are the yellow wires connected to ground (other than the generator is grounded inside, and the rectifier is grounded)? The pics show they are connected to the rectifier.
I am completely (except for generator) rewiring a 200GT which I am going to start a new thread about. After wiring, the bike wasn't charging (just like yours). I have a 40 watt (4 speed) generator. I ran the bike off the battery and tested both yellow wires. The voltages were 13 at idle and 22 when reved. I tested both wires for amps and got 8 at idle and 8.6 when reved. At this point I assume the generator is good.
The standing voltage of my battery is 6.35. I then connected all wires, with the lights (LED) and got 6.3 volts at idle and the same number when reved. The bike wasn't charging. I assumed it was the original rectifier. I tested it using the standard tests. I got OL instead of continuity when testing the red to yellow(s). So I assume it's bad.
I have a modern 4 wire rectifier. It looks exactly like this one.
http://www.guzzino.com/noname3.html I hooked that one up and still the bike wasn't charging (with LED lights on). I tested it and found I was getting 50 Ohms from one green (yellow) to red and 145 Ohms on the other wire. I don't know what the Ohms should be but I know they should be consistent. Surprisingly I concluded that the new modern rectifier was bad.
I used a third original duc rectifier. This one had continuity from the yellows to red. When running (with the LED lights on) the voltage started at the standing battery voltage (6.3) but then started going up. After a few minutes the voltage was 6.5 at Idle and 6.65 volts when reved. A perfectly working 6 volt system would show 6.7-6.8 volts with the lights on so I'm not that far off and am concluding that the system is now working correctly (or as well as it can with the original equipment).
Have you tested the voltage at the battery when running with everything hooked up and the lights on? In the pic where you are getting 6.5 volts where the rectifier is grounded to the battery is close to what you want. Connect the rectifier to the battery and test voltage at the battery. I would also test the other yellow wire for volts and amps. See if the numbers are consistent. I would check all grounds.