First things I would check are the vapor barriers in the doors. It's a sheet of plastic that goes inbetween the door and the panel, and is glued/taped all around. If that seal is broken, it will allow water to get into the car, usually pooling up in the rear footwells. Also check the gasket around the air intake for the heating system in the cowl, by this age in the MKII's it's usually not sealing too well anymore.