Water in fresh air box

It could be as simple as a blocked drain. There are small holes on each side of the cowl you can clean out with a bent wire, or if you are really flexible and have a small arm/wrist, then you can reach up through the vent and try to see if there is a build up of debris you can remove that way.

Unfortunately, most of leaks coming through the vents will be rust in the "hat" that prevent water from coming in. In assembly, those areas normally received very little primer/paint resulting in rust holes. Get a flashlight and look up in your vents and see if the wall of the hats have holes in them. If so, you may be able to temporarily fill them but many times it will requires major surgery to fix.