Are you using something to hold your camera, like a tripod, and some kind of jig/fixture to hold the film in place? Ideally you wouldn't need to touch the camera and the film would be positioned consistently between shots. Without some kind of setup scanning will be very fiddly as you need to be perfectly centered/squared/etc.
Could the camera possibly be moving some between shots? Are you shooting wide open?
As for focus changing with lens rotation, that would indicate something in your lens lacking axial symmetry. An uncentered/decentered element, an element that's not ground just so, etc.