PWM is a great way to go. The only reason I like a switching regulator better is because you don't have to compensate for battery fade. However, PWM is the most efficient regulation method, so not only do you have a very high capacity mod, but you are also maximizing run time with a very efficient regulator.
Not sure I understand how you handle charging. Did the unit come with that charging system or did you add it?
That's one geat thing about this unit, it came with a charging system built-in (see pictures 2 and 8 in OP) .. that's the main reason I want to work with 11-12v feeding the PWM, it is already set up for charging (even wall wart charger included). If I removed one of the 3 batts, it would probably be easier to regulate. However, the charging circuit is designed to recharge 3 batts in series, I would have to gut it and figure out another charging circuit.
Incidently, I am not grabbing the 12V as an output from the circuit board, which has a 2a limit. I am taking b+ and B- directly from the battery series, using the original circuit board only as a charger. Works great as is, however, it will be going PWM (though I don't think I am in a big hurry) just because it will be much more efficient. I love how it turned out!