If you can only get the top or bottom of the image in focus, it would seem to me that your camera wasn't re-mounted precisely parallel to the film. You may want to try shimming or otherwise adjusting the camera mounting to bring it parallel.
As for scratches, others have wrapped the film guide posts with soft cloth, and even replaced the plastic guides with metal or plastic guides that actually roll as opposed to the stock non-moving ones.
As for scratches, others have wrapped the film guide posts with soft cloth, and even replaced the plastic guides with metal or plastic guides that actually roll as opposed to the stock non-moving ones.