Small leaks, drips, I wouldn't worry in the least about. They take water on from everywhere. Weep holes in the headers, shorty headers not quite over the transom, even SHOULD be dripping some water from the packing in the front of the jet pump. That's what the bilge pump is for. It's gonna take on water from most all of these sources, let alone any other reasons.
What GT said may take care of it, but remember 2 things. If you tighten up things completely water tight on that, steering the thing is gonna be a byatch! A boot, I dunno, would seem to me a place to hold water, then rot everything out quicker, cables and such.
Ray