If the screws holding the rear bonnet hinge bracket penetrate right through the wood frame, as Dave says it can leak there although I wouldn't have thought to the extent you have. It is dropping just into the foot wells or on top of the gearbox cover? On to the back of the instruments or further forward?
The heater box draining can get either blocked or overwhelmed in heavy rain and cause water in the foot wells although there is usually evidence on the top of the gearbox cover by the radio. Water coming through under the screen seal and then back to the heated screen cable holes in the scuttle tends to fall right behind the instruments. Straight down into the foot wells and I'd suspect wiper gaskets or washer gaskets leaking or possibly top bulkhead gaskets. I've smeared Vaseline around gaskets etc in a successful temporary attempt at stopping leaks!
Good luck.....it's not a lot of fun
