Got the answer to the problem of wet rear footwells!

This is for my Cab although the same may apply to tintops...
The problem isn't with the door & window seals as i thought, although I still couldn't figure out how the front of the car was dry while the back was soaked. I checked the drainage holes on the scuttle and cleared these out as this is a well known source of leaks and would explain your wet passenger front footwell DJ G.
However, how was the water getting from the blocked scuttle into the rear footwells?
If you peel back the carpet you'll see the answer. VW thoughtfully built some channels into the floorpan which run from the bulkhead, UNDER the crossmember under the front seats and finish in the rear footwells. Water comes down the inside of the front bulkhead, gathers in these channels and then runs to the back of the car, gathering in the rear footwell where it then soaks into the carpet.
Lift up your carpet and mop up any water you see - be warned, it may stink! Just make sure you keep the scuttle drainage holes and infact the whole scuttle area totally clear of leafs and general crap and if you can, park the car so the front is lower than the back.
Hope this helps.