[macojoe]

Short answer is remove the screws and 4200 them as said above, this will stop anymore water getting in there.
But for the long term fix it is going to need to be cored, what has happened is water has soaked all the wood and it is rotted there fore giving you the tea colored stain as stated above.
The best way to fix this is not thye easiest but is doable. You will have to remove the windshield and the rub rail and all the screws around the hole boat, then lift the cap off and lay it upside down on the ground. Now you will be able to cut the glass off and remove all the rotted wood, replace with a full piece od plywood not all the little squares your going to find and reglass and put it all back toghter again.