Hmmm...see if you can get VDC output for that model engine from a service manual. Sounds like a failed voltage regulator which could very well be integrated with the alternator - perhaps someone can confirm that. The charging circuit is rated at 50amp for that motor, output voltage should be 14.2 to 15 volts for charging standard lead-acid batteries. Put a multi-meter on it and see what you're getting with the engine off and running.
Mine puts out 14.4 on charge, 12.4-12.6 on the dash gauge at full charge, 12.6 to 12.8 with a meter on the batteries. The latter is considered full-charge for a lead-acid battery. They generally don't drop any over a couple of weeks sitting.
Frankly, I don't think your battery change over has anything to do with your charge voltage. It's probably why your old batteries failed, if that's the case.