Since my CJ3A is 12V, I've never had to worry about boosting it, but that's one of the big advantages of a 12V conversion!
My old tractor is 6V, and if you try to boost it with 12V, you can let the smoke out of the VR. But there's a trick where you can put 12V onto the starter--on the starter side of the solenoid, so it's isolated from the electrical system. But this does require enough juice in the 16V battery to provide sparks. I don't know how I'd get that same trick to work on the CJ3A with it's foot pedal starter, though. (A nice thing about the tractor, is everything is fully exposed!)
-Paul
