For the past several years, the passenger side floorboard is always wet after it rains. At first, I thought it was the sunroof, so I used the weed wacker line idea and cleaned out the drains. Still wet. I then went a little crazy with the caulk and sealed up everything that looked like it might leak water when driving in the rain. Still wet. Finally, I gave up and took it to a shop (in fairness to myself the timing belt had also slipped a tooth). They said the leak was the sunroof drains, and they had cleaned them out. Last week it rained like crazy and the floor board was still wet! I finally decided to catch the leak in action and pulled up the carpet, etc, put a towel where I thought the leak would be, and waited for the rain. When it rained I sat in the car and saw this:
Well it certainly wasn't the sunroof!
I took off the plastic cowl cover and discovered the culprit! The air intake for the A/C system!
The cracked rubber on the cowl cover was letting water in, and it was getting into the A/C air intake.
It looks like the cowl cover has two trays to divert water away from the intake.
In the case of mine, one looks like it is supposed to "hook" under the windshield glass. Sadly, all the clips to hold the cowl cover to the windshield were broken. I decided to brute force and just seal up the rubber with some black silicone.
In retrospect, I think if I had put the cowl cover back on at an angle it might have realigned the water tray to be under the windshield and catch/divert the water leaking through the rubber seal. Oh well, it poured rain yesterday and no more leak! Hopefully this helps someone else, I'm surprised more folks don't have this issue... of course the first reply to my post might be a link to a whole thread on this topic.