I get the same problem in the drivers footwell.
Again, no rust under the bonnet anywhere, perfect screen seals and perfect door fit with all rubber stuff as new and intact.
Sunroof drains are working and the sill drains are clear and dont collect water.
Its doing my head in. However, if I run my hand up behind the front wing drip panel I can feel a hole, hidden from view and easily missed by MOT testers and the like.
I'm 'assuming' this is the entry point but I wont know til I've found a way of fixing it without cutting a wing off! (possibly reach from the inside behind the speaker pod?).
I had a mk3 that rotted in the same place (behind drip panels) and had no battery tray or fusebox tray to speak of. Good old Ford and their built-in water traps.