Need Mech Brake Advice and pinion/ motor shaft help...

Maybe a Tekno long shank pinion will solve your woes. It is still going to put similar stresses on the front bearing but should be a little easier on the shaft since it will move the set screw further down the shaft.

Anyway is that the rear brakes. If so I think you can loose a disk IMO. Majority of the braking is done by the front but that also depends on your driving style and setup of the buggy. I would try with only one rear disk and a Tekno long shank pinion. I think that should work. Anyway try before you buy. No need getting parts like the brake disks/pads if the standard ones will do the job.