Here is a crude drawing of the joint as I remember it.
Does this look like your boat?
If so, I don't think fiberglassing is the answer. You can grind through the gelcoat on the top of the bulwark and get a good bond there .... and a reasonable surface area, but you won't get much contact area with the hull.
The only glass to hull contact area will be along the ~3/8" thick section of the hull that extends up, slightly above the hull flange.
There are three places where water can be getting in.
1.Between the mating surfaces ... i.e. between the bottom of the bulwark and the deck flange. The deck was supported by two chainfalls and lowered onto the goo covered hull flange. It was easy for a little movement during the process to create a goo starved area. They gooped it up pretty good, so this isn't the most likely scenario, but it would be the hardest to fix. You might be able to tell by inspection of the area if this is what is going on.
2. There could be leak(s) around the bolts that go through the hull to deck joint. If so you might be able to remove and re-install the offending bolt(s). If not you would just have to take extra care to bed well under the teak in that area and not squeeze the goo out when screwing down the cap rail.
3. The most likely culprit is the screws that secured the cap rail to the fiberglass bulwark. The top of the fiberglass was rarely flat. The goo was supposed to fill any irregularities. Over time there could well have been enough flexing to loosen some of the screws, and/or slightly enlarge the hole(s) through the fiberglass.
The good news is that this would be the easiest to fix. I believe the cap rail was installed with #12 self tapping screws. Use #14's when you re-install the cap rail and
carefully plug the now larger holes.
I know you want a better, or longer lasting solution, but I can't think of one. Perhaps someone else can. But I don't see you having access to enough area on the hull to make a secure, long lasting fiberglass joint.
Edit: After I posted I noticed that my arrow somewhat obscures the extension of the hull above the hull flange.