Consider tying both front and rear brakes to a common master cylinder, in your case on the right bar? Polaris does this with several of their sport quads - pedal is rear brake only, lever is both front and rear - the rear caliper, if i recall, actually has two hydraulic inputs - one from the pedal master cylinder, the other from the handle's master cylinder... a transplant of some of their hardware (say from someone parting out a Scrambler) might just do the trick for you.
'01 660 Raptor, Burgard +2+1 arms, YFZ Shocks, LSR anti-vibe, CTR pipe, jetted, K&N
'01 Polaris Scrambler 400, K&N
'02 Honda 400ex, Big Gun pipe, jetted, K&N, Lonestar +2 A-arms, Lonestar anti-vibe
'02 Honda 400ex, DiamondJ +3 A-arm widener, Lonestar anti-vibe