ah the joys of a mk2!!!! we have all had it.

Mine was leaking through the vapour seals badly I used drop sheets and wurth "dap off" to seal the vapour barriers.

I also sealed every grommit im the rain tray! and got my windscreen rust removed.

Finally to top it off I bought a prestige car cover which is 100% waterproof just for those monsoon nights!

check this thread mate, it will give you some spots to look at

http://forums.vwvortex.com/zerothread?id=3666968