TT,
Generators...HRL territory! I truly don't know squat about generators, but I would be highly suspicious of using a regulator designated for six volts with a updated system putting out 12 volts. The regulator is just a voltage sensing switch..I think if it were adjusted to "switch" properly to control a 6v system, it wouldn't accurately control a 12v system.
The very least I would do is take a battery voltage measurement with truck at rest, and another with the engine running at whatever RPM would equate to charge. You will want to see a marked difference. Everything might be working properly, just not "enough" properly.
Stuart