Put your multimeter on AC volts, 20 volt range. You figure out how to do it, but get the meter leads across the yellow wires coming from the stator. What you measure on AC should be about 0.7x what you read in DC plus a couple of diode drops....light load, 0.7v each assuming a full wave bridge rectifier which I think all OB rect. are such. If those voltages relate to your DC readings at the rpms mentioned, then I agree that you should go after the charging circuit stators.
The other thing is you need to be above 1k rpm before you expect any kind of charging...per the manual.... mine. Yours should be the same.
So assuming you are at the 13.5 VDC level. 2 diode drops is 1.4 so now we are up to 14.9v for the input x .7 for the RMS (Root Means Square) value = 10.4 VAC. If your meter reads that your input is not adequate.
However, this is all hogwash if you have a heavy load somewhere in your boat......as I said, "light load". If your engine has the 9 amp stator....black as I recall, and you are running a couple of volts low then using Ohm's law, power dissipated = voltage x current. 2v x 9 amps = 18 watts. Something somewhere may be consuming that power. A Tractor headlight, for comparison consumes 35 watts. A boom boom box at least that. A shorted/partially shorted cell in your battery could do just that and would be hard to catch if all the rest were up to par. You ought to be up around 14.5 volts or so at WOT. 14.5/6 cells = 2.4v....close enough if the cell is lazy.
I assume you have had your battery load tested and it was fully charged before you ran your new regulator performance test.