Ok, I've been there done that.....
Hey,Well, its no easy fix. I replaced my entire cockpit floor two years ago. My boat was still in the water, in the slip, and I did mine right there. This did present a problem when it came to how I would do this, being the boat would still be in the weather, I did not want to cut away the top glass, but in the right working enviroment, that would be the easier way to go at it.I cut mine away from the bottom up. Removing all wet, rotted and delaminated wood... basicly every bit of it. Got everything down to the upper fiberglass layup and rebuilt it from below. Used Marine grade plywood, 3/4 inches thick, cut into small pieces about 6x12 inches or there about to fit and contour the shape of the cockpit floor. Glassed in the new wood, filled all cracks between wood with thickened fiberglass and then laid up strips of fiberglass matt and woven until I had recovered the entire floor with several layers. Then recut the hole for the pedestal and emergency tiller access hole. I also raised the mount for the pedestal so water would flow around the base and not in... just in case the caulk failed again.. and it will. That is what caused the problem in the first place. I will post pictures later tonight or tomorrow of my cockpit so you can see the finished result. I will be happy to talk with you further if I can be of any help.. good luck, big job, but mine turned out very strong and nice. Also, after cutting new holes, I glassed around the edges of the exposed wood so that everything is protected from water even if it leaks again.