Newbie with a couple of problems

[T25alfa]

Hi there,
I've just bought a 1996 passat estate. 1.9 td. (AAZ) Hopefully to run on WVO.
Currently got a lot of water in the back footwell drivers side and I can see water coming in the back passenger D post through the circular hole in the photo attached. Also some in drivers footwell.
I've read quite a lot on the various forums that seem to suggest the rear window seal. This appears to be bolted in but also glued. Is this normal. Do I simply cut the silicon seal with a wire and then clean it up and refit it with a fresh bead of wet silicon? And is there a torque setting for the nuts as I'm a bit worried about shattering the glass.
Can the water migrate from the back passenger side to the drivers side foot wells? The bulkhead drains are not blocked and door doesn't seem to leak via the door card, maybe a few drops with the hose on it.
The other problem I have is it cutting out whilst driving. This seems to be related to what I think is some sort of fuel cut off / imobilizer on the injector pump in a black box held by 2 torq screws.. Whilst fiddling with it clicks a lot and removal and refitting got us going again. Can I simply remove this or wire it up permenantly to 12v. I wondered if this could be switching off as a result of damp in or around the ECU if it has one. ( not very familiar with it yet).
Any suggestions would be really appreciated.