Well after the rebuild, I thought the caulking under the rub rail had separated so I re did that good and don't see any water coming in that way.

After a heavy rainstorm I opened the engine cover and there was a good amount of water in the bilge. Is it safe to say my cover is toast? How much rain water could you expect trough the front intake louvres? The cover is about 8 years old. Luckily the boat is on the trailer with the larger cover on top.

Here is the odd one. Somehow there was water in the battery tray which is in the ski locker and the tray is fiberglass so the water could only come from above. I am baffled but I am taking a guess the water has found a path through the tarp/windshield area...

Also noticed small amounts of water coming through the rub rail and is getting trapped near my new foam by the exhaust outlets. Looking from the inside the fiberglass is wet where the deck/hull meet but mainly in the rear ski locker area. Notice this when the boat is on the trailer with just the single cover. As I mentioned, there is more than enough silicone on the bottom side.

Any thoughts??