This first post was edited to bring the primary analysis , summary and test method to the top. Everything following that has been discussed that is relevant to the analysis has be added here.
GS Power and Grounding Scheme
Here is an analysis of a preferred GS power and grounding scheme. This probably will diverge from your original GS wiring as well the conventionally wisdom.
The first step is to re-look at what the shunt R/R is really doing. Initially my original thought was that the R/R is shunting current to ground. We it is sort of but not how I originally thought. I was struck by this when I was reading the manual charging system description. Then it because obvious that because of the combo Rectifier and Regulator the R/R does shunt current, but there is a continual load current that it has to sink through its’s negative (black lead). Sinking current means the R/R has to absorb this current direct it back to the stator through the lower legs of the diode bridge. Well big surprise this changes the ball game as far as establishing a proper single point ground.
Analysis:
Here is a summary of the elements of the physically schematic:
a.) I used the current measurements I previously measured along with a simplified version of a typical GS charging system to illustrate where the proper power and grounding connections should be.
b.) Generally at 3k RPM the GS charging system puts out about 12 amps with about 2 of those amps going to charge the battery. The various loads receive the remaining 10 amps.
c.) In the physical schematic, the stator produces A/C power, that is rectified in the R/R producing DC (12 amps) out of the red R/R wire. That power is split between the battery and the various loads (10 amps for load; 2 amps for battery) in the fuse box (I ignored the ignition switch which provides a detour to switch the various loads prior to the fuse box.).
d.) Another interesting feature is that most of the load current return paths are through the frame. In fact some GS schematics I looked at did not even have anything other than the large starter ground strap connected to the negative side of the battery.
e.) I also showed conventional direct connections between:
i.) the R/R + (through the fuse box) to the plus side of the R/R as well as
ii.) a direct connection between negative leg and the battery.
iii.) R/R (-) tied to its’ own case at the mounting bolt.
f.) I also added a R/R ground to the frame. As it turns out this is very important to reducing sensitivity to connector corrosion and high connector resistance. Since the load return current has to come back into the negative side of the R/R to return to the stator, the primary return path should be back through the frame to the frame grounded R/R !!!!
To be clear, the R/R is not shunting current to ground (i.e. to the frame or the battery), it is absorbing load return current from the path of least resistance. That should be the frame ground attached to the R/R. If that R/R negative leg is not grounded, then the only return path for the load current is either
a.) a direct connection of a ground wire from the harness to the negative side of the battery and then back to the R/R or
b.) a frame ground path back through the motor mounts to the battery via the starter ground strap and then finally top the R/R on the R/R ground to the battery.
It is important to note that the R/R attempts to regulate based on voltage it measures internally which the best we can tell is the voltage between the red and black leads on the R/R. Any current flow between the battery and the R/R tends to reduce the voltage that the battery sees because of voltage drops coming from the positive side or from the negative side. Minimizing the current flow from R/R (+) to the battery or from the battery back to the R/R (-) helps keep the sensed voltage more accurate.
You can reduce the return current from the battery by providing a good frame ground so that the bulk if not all of the load return current come through the frame to the negative side of the R/R.
On the positive side of the R/R , the full 12 amps goes to the fuse box. Any resistance there will cause a voltage drop (from 12A) and erroneous regulation. If you can not keep that resistance low, then put in a separate fused wire directly from the battery to the + R/R. It is this resistance on the positive side that can cause the fold back where your full R/R current is going through a relatively small resistance and causing voltage drop off at the battery at higher RPM.
Summary:
So what this analysis suggests is that:
1.) The R/R (-) should be SOLIDLY connected to frame ground.
This avoids current sharing between the 2A charging current returning from teh battery and the 10A load returns. By having the R/R grounded the voltage sensetivity to resistance between the R/R (-) and the Battery (-) is 1/6 (i.e. 2A v.s. 12A)
2.) The battery should NOT be connected to frame ground.
This causes current sharing as described above in 1.)
3.) Other than the starter/solenoid connections (pos and neg), the battery + should only connect to the positive side of the R/R and the battery negative should ONLY connect to the negative side of the R/R.
minimizing the current between the battery and the R/R on both (+) and (-) side reduces teh errors described in 1.)
4.) If the resistance is low enough the R/R (+) leg can go through the fuse box (to teh battery +) but be careful of getting voltage drops from the full 12 amp supply current.
If you share the 12A coming right from teh R/R (+) to the Fuse box keep any resistance to a minimum becuase it will cause more drop than just 2A of charge current alone.
5.) If there are spare load ground lines they should be tied to the R/R ground or to a frame ground. This follows from a single point ground philosoph where all currents shoudl return directly to the R/R (-). The frame is god enough or go direct to teh R/R (-) if it is closer than a frame ground.
Comments welcome.
Pos
Edited Verification Tests:
A simple point to point list for you:
1.) Three wires tied together at a mounting bolt for the R/R at the side plate. Note this is not a frame ground point because the R/R is mounted on a plate mounted in rubber. connection 1C performes the frame ground.
a.) R/R (-) from the black regulator wire to ring lug on a mounting bolt
b.) Battery (-) to a ring lug on the same mounting bolt
c.) Frame ground strap from mounting bolt to frame (not the rubber mounted side plate)
2.) R/R (+) goes to the fuse box as normal
3.) Only connection other than 1b above to battery (-) is the 8 guage wire ground strap to the engine.
4.) For a Honda Regulator connect your sense wire as suggested by Duanage
For the following discussion:
V_negative is measured from battery (-) to R/R (-)
V_battery is measured directly across the battery terminals
What you should notice if you omitt 1c above is the following:
The wire from the battery (-) to the R/R common ring lugs should carry 10 amps at idle and 12 amps at 3K RPM.
V_negative should drop and will likely be between 0.25-0.5V.
V_battery measured across the battery terminals should be something like 13.0V at idle and rise to 14.0V at 3K RPM.
After reconnecting 1c above you should notice the following:
The wire from the battery (-) to the R/R common ring lugs should carry 0 amps at idle and 2 amps at 3K RPM.
V_negative should drop by at least about 1/5 of what ever it was. If it was 0.5V it should be 0.1V.
V_battery should rise by what ever the change in V_negative is. So 13.0V will turn into 13.4V.
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Crap Crap triple crap 
