If you can do this, which I am sure you can with time and money, only the front axle and the rear axle will have the yoke not being used. The middle axle (or front drive axle) will have a drive shaft connected to both sides. That doesn't mean you couldn't fashion some sort of brake on it as well in-line with the drive shaft though as there are applications out there with this setup.
If you do get the rotor setup lined out you'll have to tackle the mater cylinder side of things. You'd need to check bores of the master cylinder and whatever brake caliper you use to determine if the master cylinder could provide enough braking force to the whole system. Also keep in mind that disc brakes "consume" fluid or the volume of as they wear whereas drum brakes have the adjuster on the backing plate that takes up the difference between the brake shoes as they wear so the wheel cylinder strokes the same amount
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