It's so strange. Underneath the windshield cowl is a tray that allows water to drain down the passenger side fender and onto the ground. Along the tray is a hole with an approx 1" high wall around it that is used to suck in fresh air to the blower fan, which can be seen down the hole. It doesn't appear that water is getting into the hole because the wall stops it.
It looks like the water goes past the fresh air hole, then down the inside of the fender, at which point it somehow gets into the cabin. Is there a diagram or picture anywhere that shows what is behind the passenger side fender?
Edit: Found this thread on honda-tech that looks like the same issue.