I binned the stickers. I removed the vents, left them to soak in hot water with washing up liquid, then I used stick stuff remover & IPA to clean up the areas around the stickers & vents. I used some spare plastic divider inserts that you get in those DIY storage boxes, cut them to size & used Puraflex sealant to stick them on. The vents went back on ok without the Puraflex. They didn't leak when I sprayed water over them, but not to risk it, I gave them the Puraflex treatment as well. I let the sealant set for a day & tested the new seals - all was well.
The tyre well had about 3 inches of water in it so drained it & checked the carpet, which turns out was sodden. I got the carpet & underlay out & dried it out (took nearly 2 days). I siphoned the water out, & luckily, no sign of rust on the floor pan so made sure it was dry & put everything back.
....then it rained. The tyre well had filled up again.
The seals I had just repaired & the seals on the light clusters all checked out.... 
Turns out it was the lap joint between the roof panel & the top of the rear pillars for the boot. The pic shows me shoving a store card into the joint to highlight the gap but the gunk that was the sealant had separated & I couldn't see it until I pressed down on the joint & saw water squeezing out. Most of that joint (from the roof channel down to the rubber surround of the boot) had separated. I managed to get most of the old sealant out, dried it as best I could, then squeezed in some Loctite silicone gel. It has rained pretty hard many times & no water is getting in. I wonder if the original sealant is just weather-proofing or if it serves any structural bonding function, adding strength to the joint.... I bet it does
Another water test & the tyre well stayed dry so, hopefully, that's the end of it. Although I've got the roof bars to do (that'll be another write-up) & I've read that when fitting (& if removing), I need to make sure the bolt holes are well sealed, as it's another poor design - more Puraflex, I reckon.