If I understand correctly, you set the lens to infinity, and then check whether the double image aligns?
If your camera is misaligned and adapters and lenses correct, you'd get the same amount of misalignment with each lens, as the RF cams should push the RF roller equally far in this scenario. So you can basically rule this out.
Next, if you use three different adapters but the lenses are okay, then there could be something wrong with the thickness of the adapters. If the problem persists if you keep a single adapter on the camera and merely screw in/out lenses, it's the lenses.. The 35 + adapter work, so that's your golden reference..
And when it comes to the 50 and 90, there's a whole list of things that could be happening, depending on model and vintage, some of which are:
- Very old FSU lenses have RF travel that doesn't match Leica. They should line up at infinity, but..
- The lenses may have been re-shimmed for another camera, or
- The lenses may have long focus travel, whereas modern Bessas like short travel best. You can see this in the form of different focus when coming from infinity or from closest focus distance.
- The cams of the 50 and 90 could have been worn down from running on a camera with a shoe RF coupler instead of a roller
And I'm sure this list isn't exhausted..