In clear water the alternator usually will survive. The dirt/mud/grime is what tends to kill them. As far as the noise, I would check all external moving parts that were submerged. More than likely they have grit in them which is grinding in the bearings. If you were that deep you will probably want to change your diff fluids also. They probably took on some water and it doesn't take much to break down the lube and make it less affective.