any mk3 will have the wires from the light switch to the front connector in the engine bay wiring harness, but fogs were never standard iirc - you're talking about VWs here, the options list has always been longer than a roll of bog paper.
you'll need the light switch with fogs and then just need to connect the fogs in the engine bay to the wiring harness connector that sits above the radiator (all wiring from the light switch to there is already in every mk3). all you need is a male spade connector, think 4.8mm wide, crimp that to a 2.5mm2 wire, this goes to pin 5 in the harness connector.
see here for which on it is:
http://forums.tdiclub.com/showthread.php?t=288640from there you can split the 2.5mm2 line to 2 x 1.5 (1.0 will do as well) and go to the fog lights, second wire on fogs you can hook up to another 2.5mm2 and go straight to negative battery terminal.
don't cut the wire before the wiring harness and dodge it together... you'll never get loom right again.
will send you a photo of how i've done mine tomorrow.
what do you mean you got water coming in from door?? even without a membrane you shouldn't get too much water in. a bit yes, but not streams unless there is torrential rain and you're in a river.
but does not help if there's no membrane, so as a first step try that. to fit it i would use something like '3M 8008 super weatherstrip adhesive' (it's a rubbery kind of glue that is flexible and will stick quite well to metal and not dissolve or degrade membrane). would advise against silicone since acid it releases on cure will cause corrosion and make plastic of the membrane brittle. so won't doing you any favors.