Forgive me for being a "Morgan Owner in Waiting" but why are the footwells so leaky?
When I first had my car the footwells were getting wet. Silicone sealer between the frame & floor has almost eliminated it & that was only under the seat & immediately in front of the seats not all the way to the front. I dont think much water gets in from above but I do drive with the half tonneau on most of the time. You do get plenty of dust but sealing behind the seats helps a lot. I think the cockpit is a low pressure area so you are unlikely to stop all dust.
Tim