So, I want to thank you formally here. I lifted the boat out of the water this past weekend to check the exhaust. There was zero leakage from the exhaust, even when I tipped the boat back. I also put a ton of water in the bilge to see if I could get it to come out, but none did. I snugged the clamps on the flaps, as they were a touch loose, but that's of no consequence.
With it in the air I got a good look at the under side of the rub rail. There was a significant gap on the right-hand side, and a bit of one on the left. It looks like it had been filled using cheap clear silicone and it had come out, and had separated away from the rub rail, some of it completely gone.
Hit up a local marina that actually had the nice white 3M Rub Rail sealant and adhesive and did about the last 4' of the boat and 1' around the back (the whole boat needs to be done, but this was the area I was concerned with) and took the kids out for a tube. Boat stayed dry! Didn't take on ANY water.
Also, worth noting, the front-most fin; the fin just below the tower, was extremely loose. I tightened it down as well as part of this. I assume this was my persistent leak when the boat was sitting. It appears to be staying dry now.
So, that problem is solved! I'm going to start a separate thread about the transmission, as that's our remaining issue with the boat.
Thanks again!