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There have been some similar problems with a few boats before. You can probably find them with the search engine on this site using the toolbar above.
Your boat's hull has a transferrable five year hull warranty, which will still be in effect.
I don't see a dealer listed in Juneau, and the nearest one is in Anchorage, way too far to make a trip reasonable for such a problem.
What I'm going to suggest is that before you do anything, you contact the factory rrepresentative, Jeff Messmer, at the C-Dory factory <jeffmessmer@c-dory.com> or (253) 839-0222 to see what he recommends. They have delt with this problem before and know what works as a fix.
Some thoughts on the issue:
Absolute drying would have to take place to seal it from the inside or outside, of course.
Patching it on the inside would be the simplest solution, but might not work in the long run depending on the hull flex and how tightly the 3M 5200 will adhere to the inside surface of the hull. Not a good choice in my mind. Thie screws need to be sealed all along the threads that protrude into the hull material.
If removing the strip were no big deal, I'd favor that approach so that you could throughly get the 5200 (or even 4200) in to seal it screws off good. (4200 comes apart more easily, should you ever have to loosen the rub rail for replacement or for some other need).
It well might be possible to just pull the screws out, shoot sealant into the holes, re-insert the screws, and let the hydraulic pressure created by the screw replacement force sealant into the leaking area. You'd have to get it right on the amount of sealant: too much and you'd push the inside of the hull out further (and also bond the metal rub rail to the hull excessively), too little and the seal would be compromised a bit. Check each one out as you start and see that you're not overdoing it, but at the same time getting some minor amount of sealant inside through to the leaking area that can be wiped down.
I'd also consider cutting off just enough of the tips of the screws to help stop them from lifting the inside surface of the hull so much.
If I was unable to uniformly control the sealant coming in from the outside replacement of the screws, I'd also go inside and seal that surface with the same sealant.
Have you checked all along the rub rail from bow to transom on both sides of the boat for any other leaking areas?
Hope this helps!
Joe.