I definitely will be contacting them regarding this. The idea is to be a bit informed before they jump to conclusions and repair the wrong thing, wasting weeks of everyone's time. I did notice that the drain holes in the area just below the windshield were plugged with many leaves etc. I'm also thinking it might be the AC, although I haven't heard anyone else complain of wet passenger footwells caused by the AC.
I've been drying things out and will try to determine the cause.