Sorry to come to this thread late, but I have had similar maddening issues over the last couple of weeks. Drivers footwell puddle overnight after heavy rain. I have had the dash top off, the scuttle cover off (clear of leaves), checked the pollen filter (dry) and fan box (dry and leaf free), checked the air con drain pipe (clear). On advice, removed the nearside inner wing protectors and washer bottle to check inner wing etc etc. When it was happening, I could hold a hose just ahead and below the screen and to the outside of the bonnet hinge plate and see water running into the footwell from a box section just in from of the door pillar. I just could not see where it was coming in.
Then.. it decided to stop leaking last week. Even with torrential rain on Friday and Saturday it was bone dry. Parked in the same place as when it had been leaking like a sieve. I just don't get it. Loopy theory I am clinging to is that having driven through so much standing water, there might be some section of inner wing that might have "filled up", so exposing a route ini for water - and once we the floods and rain had stopped for a few days, the water dissipated. I don't know, but I would love to get to the bottom of it too.
Dom