That's all good info but his car has a full vinal top and I did think that the qtr windo could just be reinstalled easily after removal. Someone else with landau experience will need to chime in.
My Regal used to be a vinyl top before I removed it, the only difference is that the trim around the glass is cut shorter. However, the glass still seals directly against the body with no vinyl in the way.
One other possibility is there could be rust holes under the vinyl top allowing water to leak in. The factory performed much poorer bodywork on the roofs of vinyl top cars because they knew the vinyl would hide it and to cut costs. It is not uncommon for landau roof cars to have rusted out roofs hiding under the vinyl. As I said, I removed the landau roof off of my car and saw what a crappy job GM did on its roof, Ford and Mopar also cut corners on their vinyl tops like this.