I had a similar problem. The water was originating from the wires going through the cockpit floor. Water tracks along the steering and throttle cables and runs down onto the rear birth fiberglass ceiling shell. In a very heavy rain, the water can actually swell over the small pipe in the floor and frankly flow into the birth ceiling. Seal that hole and you should be good.
I used a rubber baffle and marine silicone. Dry ever since.