
The likely candidates for the water are the aerial grommet and / or the 3rd brake light seal, both easy repairs. If you move the boot carpet next to the passenger side rear light and stick your hand in the hole behind it you will find a well and I would put money on it being full of water, you will need to empty it there's alarm units in there, tilt sensor I believe that will most likely have rotten terminals, you can easily do without it so don't panic if its knackered.
As for the window, that depends if its an original zip in window, if it is then you can replace it, but I believe its a total PITA to do. If its a sewn (roof not OEM) in then the only real option is a new roof and that's what I would do regardless, a new roof can be supplied and fitted for circa £350 by Jack Smith in Swansea, you will find many posts on here referencing his work.
That’s really helpful thank you. I’ll get in touch with Jack Smith and investigate my boot further! I’ll have to wait until the rain stops though which could be a long time.!
It’s actually an original zip in window but I’m much too amateur at it to try it myself