Wow, thats weird! I plan on replacing mine this spring when I repaint. I know the first thing I would do is open up the engine access doors and listen for any whinning coming from the alternator/belt, tranny and where the shaft leaves the vessel to evaluate any sound from these locations? If its not from the engine area then it has to be the skeg. Could the piece have been installed offset? Perhaps it a different inside diameter sufficient to cause friction? What was the old cutlass bearing like? Is the sound metallic? If you did not have this issue before you had the work done, I certainly would get those who did the work on the vessel immediately to fix the problem.
Good luck and please let us know how it turns out.
Bob
'88 Mark II