Water Leak 1995 Ford Mondeo to rear passenger footwell?

I have a water leak somewhere which is leaving water collected in the rear footwell behind the drivers seat and have noticed a small gap of approx 3mm between the rubber window surround to the rear door nearest the central pillar. I have tried pushing the rubber to close the gap but when the window is wound up again the gaps simply reappears. I'm not sure even if this is the source of the leak as I can't see how a leak in the door could find its way across to the rear passenger footwell. The only other thing I've noticed is that the rubber joint in the roof (which runs parallel to the side of the car but inset about 3") above the passenger footwell seems a bit loose. Could this be the source of the problem?

Has anyone else sufferred this problem and found a solution? Any help on how to fix would be appreciated.