3) Door seal
The door seal is a push fit onto the flange around the door aperture. If it isn't properly located then water that runs down the gap between door and windscreen, ie. outside the seal, can seep under it - usually at the front lower end where the seal bends from vertical to horizontal. This will run under the sill trim and into the felt underlayer and carpets.
Interesting, just had a look and had'nt pushed the door seal back on correctly after I had the roof bars on the other week! Could be that. Will have to wait for it all to dry to see.
Just cause it smokes doesn't mean its broke
*Unless the smoking is due to a breakage, then it does