I have several thoughts...
1. Did you say that your livewell feed AND discharge were below the waterline?
A very simple place for water to come in would be from the drain side of the livewell, in that situation. Even a small crack in the discharge hole would allow a lot of water in at 25 knots.
2. Have you taken the time to clear silicone the BOTTOM of your rub rail?
It doesn't take a huge, ugly bead, just enough to make a smooth, fingered bead under the rail. It's amazing how much can get in there, even when the crack appears tiny. (1/16")
3. Do you have a seacock mounted DIRECTLY to your thru-hull water pickup? That is a BIG thing, and I've seen boats SINK from the livewell pump blowing up, and allowing water in unhindered.
I hope you find it! I once had a Bayliner with a mystery leak, and I NEVER trusted that boat very much.
-TH