Update on this:
I stripped out the carpets about three weeks ago (hardest thing was getting the bloody centre console out - the plugs over the holes for accessing the bolts that hold the armrest on were a nightmare to get out). The soundproofing told the story.
Rear drivers side footwell was soaked through, and black.
Front drivers footwell was stuck to the rubberised coating over the floorpan, in places, but not too bad.
Minor watermarks on passenger side.
So, with carpets out, and able to see what was going on, I waited for rain.
It poured down that night, and when I got to work, after driving through all the standing water, there was a large puddle in the rear drivers footwell.
Aha, thought I.
Found someone with hydraulic ramps and went looking for holes in likely areas...
Did, however, ascertain that the rust isn't too bad underneath, with only a few patches where it's heavier than you'd expect. Also, with the time to look closely, it appears to have been caused by damage from using those hydraulic ramps favoured by many mechanics, with the sliding bars that support the chassis. The sill welds have bent bits where the car has rested on them, and most of the rust is in lines between the bent bits.
Happily, it looks like a wire brush, some of that clever rust killing paint and a coat of underseal should keep the rust demons at bay.
I did find two rubber seals that weren't sitting right, so they were pulled out, cleaned up, and replaced. Then I waited for more rain, to see if it had stopped the water getting in.
There was hardly any - not enough to create standing water, anyway.
But, every time it DID rain a little bit, I ended up with a puddle. (I hadn't checked the footwell on the first day of heavy rain, because it was Monday morning, and I was still half asleep when I left for work)
That meant that the water wasn't coming in underneath.
Spraying a hose over it didn't show anything up, but after each rainfall I was eventually able to work out that it was coming through the sill in the bottom corner of the rear drivers footwell.
So, yesterday, I spent an hour with a watering can; investigating door seals, hinges, and everything else on the drivers side that might, potentially let water in. And I found it.
It was getting through at the front of the sill.
Open drivers door, look just in front of the bolt that holds the bottom of the wing on, and you'll see a join.
The water was getting in THERE.
After a finger full of sealant, a night of rain has left nothing inside the car.
The only problem is that now a little bit of water pools in front of the sealant and doesn't drain away - but I can keep an eye on that.
Now I've just got to get everything back in, once I finally get the soundproofing dry again. Think I'll soak it in bleach first to kill off the mildew.
It'll be nice to have seats other than the driver's back in - although I've enjoyed the increase in MPG and acceleration that removing all that weight brought.
Next I need to sort the squeaky suspension... <sigh>