Its a long process of elimination in these cars, best done outside in summer. I took my seats out as well as the carpet and spent hours investigating the obvious "common" sites, door seals, cheater's, snorkel, door glass alignment etc.
I found that the most noticeable leaks was at the base of the passenger door just wear the seal turns and runs along the treadplate. There are holes in the seal at this point, I assume for drainage, but when the door is shut this compresses the seal as it should, but I'm sure water tracks over the lip of the sill into the cabin. I sprinkled talc around the door sills and it did show water tracking through.
I was also getting a small leak through the cheater which tracked down the door over the speaker, not enough to soak the carpet though.. I sorted this by buying a good second hand seal which runs round the windscreen and down the A pillars, washed it in in really hot soapy water and left it alone for weeks in the hope it would reform its original shape. It did to a point, but I still slid some 5mm soft rubber tube through the hollow section to improve the seal. I also replaced the Cantrail seals with new ones.
I understand brand new door seals are now available for about £200.
I also removed the rear bulkhead plate behind the seats which was quite rusty at the bottom. I'm convinced that this rust was caused by water tracking up the plate from the wet carpet over the years; as there is a plastic sheet behind the plate which was sealed and intact.
Its still not 100%, but a lot better then it was, it is difficult getting the door glass aligned properly even with new seals.
I made do without carpets for months before I got round to replacing them, and I also used my wife's yoga mat as an underlay, a lot lighter then the original. Its still a mystery to her as to where she left it.