So I was thinking...you aren't going to be able to run mechanical brakes that way you have it now. The brake pads ride on 50024 and 50074 which is connected to the D gear on the outside of the gearplate 50011. You have all that removed in order to run a pinion / spur to the center diff...which seems like the best idea.
In this picture the upper gear mounting plate is turned around to face the side that the pipe is normally on.
I think you are going to have to rely on ESC brakes...