Sorry to hear of your problem. My boat got splashed yesterday.
If you can get out and sail on a breezy day you can determine once and for all if the problem is the engine or the shaft log. Sail on windy day, turn the engine off, and put the trans in neutral. The shaft should freewheel (assuming you don't have a feathering or folding prop). If you have a leak, it's the shaft. If no leak, then it's the engine exhaust or something like that.
Good luck and let me know if you need a hand testing things.
One last thing, I don't think it will be possible for you to apply anything from under the boat. I doubt you will be able to see where water is getting, and I doubt you could apply anything that would stick and make a seal.