Well I carefully cut the underlay so that I could remove it and it's drying out now. It holds a whole bunch of water eh!
https://farm5.staticflickr.com/4864/...f125a10a_b.jpg
The floors look OK. They'll clean up reasonably easily.
https://farm5.staticflickr.com/4860/...aa3cef9a_b.jpg
I got some help with a hose to try and find out where the water is coming in. My first suspicion of the top of the windscreen seems to be incorrect. Hosing down that spot doesn't seem to lead to water coming in. The A-pillar under the plastic cover is dry, and it doesn't run down the side wall. Spraying at the bottom of the windscreen and filling the plenum does result in water coming in on the passenger side. It drips down around the heater fan. It seems to me that the plenum fills up and it leaks in behind the bit above near the bolt on the top right of the next pic. At first I thought it was that middle bolt but the water level seems to stay above that. The plenum drain hole appears to be clear.
https://farm5.staticflickr.com/4868/...69f7f056_b.jpg
I need to spend a bit of time just confirming things. I couldn't get water to come into the drivers footwell with the hose. From the look of it, it might be the door seals. It wasn't as wet nor as rusty as the passenger side.
It's all way more than I'd hoped to do, but best to get it right. I'm still having fun too. Incidentally, my kid locked the doors with the central locking and I tried to open the rear (boot) door with the door locked. Now I can't open it at all, inside or out with the lock open. Any tips on this? I imagine it's going to involve pulling the skin off the back. Annoying because the back is full of front seats etc!