I saw your post on another forum about the LED's available on e-bay. I've contacted him and after I make measurements will be getting a set. So anyway, the wires will fit in the fins I take it?
One thing I wonder about is the brightness. Won't the LED's direct appear too bright? Afterall, the 3mm LED's in the nose and under the bow fins are spotlights, while the lights in the fins are simply navigation lights?
Another tip is to grind off the tip of the LED with a dremel or file. The rounded tip helps to focus the light beam, and grinding it flat (or even better as an inverted cone) helps to disperse the light far more evenly. I use that trick on all my Nautilus builds so that the spotlights are more visible from a greater angle.