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You see Peter... now you are getting all fancy with a digital protractor. This starts to no longer sound like a poor man's rotator.
If you want to do this on the cheap and even simpler. Just plate solve one of the scopes to find out the camera position angle. Then do the same for the second scope and keep rotating the camera until you get the position angles aligned.
Put a piece of masking tape on the rotator and camera so if you remove the camera's you can quickly visually align then double check via plate solves before imaging again. If cable wrap is an issue for one camera, just flip it 180 degrees from the position angle value of the other scope. sub registration will sort out the reset.
I think I would be more worried about getting the scopes perfectly parallel so that they are imaging the exact same field of view. Again, plate solving can assist you there. You want to ensure that when you plate solve to get the fov center in RA and DEC, that that same RA and DEC is the center (or near to) on the other scope.
If one scope has a wider field of view, do the RGB with this instrument. You want the higher resolution from the longer focal length so the lum from a narrower field of view.
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