That's a good suggestion, I need to mention the car has no sunroof and was left stationary for two days on a level drive, it rained heavily. Consequently does that mean the water could only get in through the bit between the windscreen and the bulkhead? The bit under the skuttle panel where the wiper motor sits. As previously mention the screen looks original (VW marks and signs of age) and the skuttle was not properly seated.
Would someone be able to send a diagram of where to check?
Here is a pic of the scuttle access hole (plastic cover panel removed) on my car when I fitted a Polar FIS box. You have to remove the wiper mechanism to get to it unfortunately, which isn't difficult, but it takes a knack to find the right angle to pull it out! It's in there very tight.
The standard CAN gateway is the first box without the sticker. As you can see by the clean patch, that is where the seal on the cover panel sits. If that seal gets damaged, or not put back on for whatever reason, water could potentially gush in there during a heavy downpour.
The only reason I'm suggesting it's that is because the previous owner changed the gateway, and it's very tricky to get at from inside the car, so it's a likely culprit!
In each corner of the scuttle is a drain hole. If these are blocked with leaves / debris, water can back up into the scuttle area and flood it. If the water level rises high enough, it can pour in through the fan inlet (passenger side). Had that happen to me when parked on a steep drive in heavy rain, car pointing upwards.
I don't think water can pour in through the doors on the MK5 (common on older Golfs) because of the way the doors are constructed, and you've got no roof, so it can only be coming in through the scuttle area.