Was determined to find the cause of the final small water leak into the car (after replacing the pollen filter cover) before refitting the carpets. I pulled the glovebox out and with a bit of contorsionism I was looking up at the bottom of the fan unit, and specifically the closed flap for the recirc setting. At the edge of this I could see some moisture and figured there was still water getting in at the filter. So I removed the wipers, engine bay seal, scuttle panel, rain channels, pollen filter (again) and then the actual pollen filter housing. The housing is held in by two 10mm plastic nuts and a foam seal, one nut is inside the housing with the other one outside, between the housing and the inner wing area.
Once the filter housing was out I discovered this small amount of rubbish:
After inspecting the filter housing closely I could see water had tracked down the inside of the filter housing between the filter holder and the housing itself - with the height of damp leaves behind the housing the water must've been slowly making its way into the housing.
Cleaned all the crap out around the entrance to the fan unit (I hoovered out the few leaves which had fallen in when I took the housing off) - the flap you can see is for drawing in fresh air and closes when the recirc is activated ( and the lower flap opens)
The foam seal (ha!) around the base of the housing was soaking as well, water would've been free to pass through it so I peeled and scraped off as much as possible
before using some of the butyl I had left over from doing the doors to make a new seal
The filter housing and filter were then reinstalled along with the rest of the bits...
Hoping that is it now, it started hosing down about 20 mins ago so fingers crossed this is the last of it....
If not then it's getting torched/sold/broken!