I really feel like it's not the battery since I've been using two different ones with the same results.
Last night, while trying to solve my KLX 351 starting problem, I looked through all of the pages on the KLX on kawasaki forums. On the 29th page, I found a thread about this issue. Several people solved the low charging problem by simply adding extra power and ground wires from the regulator rectifier to the battery. They mentioned that they used thicker wires than stock and spliced them into the stock wiring and the problem was solved... So I may try this, it will be relatively cheap for me to pick up some 12 gauge wire.
On the bright side, I figured out my 351 starting problem (brand new big bore kit) - the starter idler gear from the flywheel gear to the starter motor was somehow bad, and causing the motor to spin slowly. IT LIVES !
Meanwhile I had to buy a new gear for my stock 250 since I robbed that part, so I won't be able to test any electronics until after that arrives.