Another Possibility......
Tony: Something else to consider as a possibility (Kevin; please come back if what I say is total BS). If you were physically looking at the prop shaft exiting the stern tube (from outside the boat I presume), I must assume that the boat is out of the water and up on stands. If the boat is indeed out of the water, then the hull is likely not sitting the same way that it would in the water, and judgements on proper shaft alignment cannot be made. However, it does sound like something might be significantly out-of-whack, and the other possibility is that the boat is not quite supported in a well-balanced manner on the stands. If the boat is not quite properly supported it could easily distort the hull shape enough to displace the shaft/tube alignment. I would check more closely to see if the shaft is actually in contact with the stern tube and, if it is, try to determine if there is any real stress; can you rotate the shaft by hand? If prior to hauling the boat your engine ran well without noise or vibration, and now you have contact and can't rotate the shaft, then I would quickly have someone from the boat yard check the jack stand support. On the other hand, if there is not direct contact, or you can rotate the shaft easily by hand, then I would consider loosening or disconnecting the coupling for the winter to prevent cold temperatures from possibly making matters worse, and do a good and proper alignment in the water next spring.Good luck.Carl