Sorry to revive this, but wanted to recap and close it out for any poor souls who happen upon this thread in the future.
The initial issue was high and irregular voltage with the stock units, spiking above 15V. This was a problem for me specifically because I "upgraded" to a lithium battery and didn't want to cook it.
I ordered a chinese reg/rec combo, wired conveniently for the stock CB350F/400F harness. However, after installing the new reg/rec, I had an under charging condition putting out sub-13V. This was due to the spade on the insulated red wire inside the harness-side rectifier connector being broken. I have seen this referenced elsewhere as a common issue. I'm guessing the insulation retains moisture? After repairing the connection I again had charging voltage, but once again too high (above 15V) and irregular even with the new reg/rec unit. I inquired with the seller and these units should have a voltage ceiling of around 14.8V. The reg/rec unit failed a diode test on the rectifier, so I ordered a replacement reg/rec unit. The second unit works fine, regulating voltage around 14V. The first unit was defective, or I toasted it being careless when troubleshooting.
Long story short, check ohms on your grounds AND your powered circuit before going on a wild goose chase. Diode test the rectifier. Pay homage to Scottly, Calj737, and their father TwoTired.