Man, I'm glad that wasn't MY procedure :-) Just kidding of course.
Does it happen in neutral? If so, you'd better check the tension and condition of the drivebelt, might try running on the trailer to see if the water pump is pushing water out the exhaust.
I'd think the sea strainer water problem (and it IS a problem) is unrelated to the whining. Gotta work on that, too.
The only whining thing I've seen is from the strut bearing/bushing under the boat when running in gear, dry, while on the trailer.
If this happens only in gear, I'd probably check the engine alignment (procedure at left) and then take it to a tech and say WTF? Sounds pretty scary to me, but then again it could be something real simple.