[Chris is me]

So back to the actual gearbox...

I think your CIMs aren't supported as well as they could be. It's pretty common in these kind of gearboxes to have a web that follows the diameter of the CIM in order to support the whole face. Right now the little sliver of metal supporting the middle of the CIM may not be substantial / rigid enough. The tiny amount of weight savings isn't really worth risking flex in that area of the gearbox.

If that is a stock ballshifter shaft, I would be concerned about direct driving a wheel off of that shaft. It might not be a good idea to load the shaft that way. The hex end of it is just pressed in to the end of the shifter shaft, with about 3/4" of engagement if memory serves. I think this is one reason the COTS direct drive ballshifters have a third gear stage. This does indeed make fitting a ballshifter into a WCD gearbox in 2 stages quite difficult.

I'm working on a similar gearbox for a similar application, and the constraint of using the ball shifter shaft without direct driving off of it is quite annoying. I don't know how feasible this is at all, but have you considered using it backwards? Having the CIMs drive a gear on the output of the shifter shaft, then putting two output gears on the wheel shaft? Might be worth a shot, particularly if you're into the latest WCD fad of hanging your drive motors over the wheels. Probably not a good idea, but something unique to look at.