Not sure if your Golf is Lefthand drive,(ie.Greater Europe/USA),or Righthand drive,(ie.Great Britain,Australia etc.),I live in Australia and recently had a very similarly frustrating experience. My Left hand,passenger floor pan would get soaked after any kind of prolonged downpour of rain. The problem ended up being a crack in the drainage tray which actually forms the lid which sits on top of the Pollen filter. It seems the lid is very difficult to manouvre in and out of its correct position without easily putting pressure on the edge of the tray/lid and potentially cracking it. A small metal tab, 2x holes,2x rivetts and a smothering of Silicone over the crack and my mystery water entry point was eliminated. Oh, and of course some very gentle and contorted effort in replacing the lid over the pollen filter so as to avoid it cracking again. Should be able to access the pollen filter from the front of the moulding which bridges between the bonnet/hood and the windscreen. It's a long shot but could be the problem.
Marcus 67
August 2009