On our custom WCD for this offseason, Grayhills 63Rs were were loosely pressed into the inside ends of the rear axles and the encoder housing was secured (so it won’t spin with the axle) by zip tying the signal wires to the frame (method found here on Chief Delphi).
I admit I am not familiar with the KOP drive train, but it might be easier to figure out how to mount them on the outer live axles instead of to the transmission? For the method I described above all you really need is a 1/4" hole at the center of one of the other live axles.
If all you need is a 1/4" hole to mount the encoder, you can attach a 1/4" shaft coupler to the encoder stub at the back end of the main output shaft. We’ve done this in the past with a potentiometer when we were making a TB-mini into a super-sized servo to steer our t-shirt cannon.
Note that there is a wood dowel inside the surgical tubing to prevent it from collapsing and twisting. There is nothing holding our custom plastic mount in place other than the tension from the surgical tubing, and the curved sides that match the profile of the CIMs. You can take the encoder off by just pulling straight back, and stretching the tubing.