Just went through this myself. After a lot of testing I figured out it was the A pillar metal on the windshield sides. For whatever reason, Toyota put three holes down the inside edge of the windshield and these were partially uncovered. I popped off the interior A pillar trim and sure enough, when pouring water down the edge of the windshield, water runs in those holes and drains out at floor level.
I had my windshield replaced in January and that's what triggered this. The windshield was sealed properly but the channel on the edge of the windshield (under the weatherstripping) had those holes exposed so water was pouring in. My glass guy resealed everything last week and filled the three holes and zero leaks since. Might be the solution.
Thanks Hokie - you just confirmed what I have spent the last two days chasing.
I have bilateral wet floors beneath my floor mats. My first inclination was a failed heater core. However, the telltale coolant feature(s) were not there. Just a musty smell and saturated carpet - water saturated.
I had INITIALLY suspected the windshield I had needed to replace in August as the culprit. Non-OEM glass was the cause I thought. I poured water down the windshield, fully expecting the firewall to become wet. Nothing. So I gave up on the windshield as the cause. But I did not suspect the reveal molding on the sides.......
Long story short - I pulled the carpet (and all the trim) out of both foot wells. Then I turned on the HVAC with (and without) the AC compressor on for over an hour. NO LEAKING. I pulled the condensate tube, flushed it out - NO BLOCKAGE. Everything appeared to be functioning within the HVAC system properly. SO I checked that off of my list.
Then I thought that after our two week trip to the Outer Banks and running around Carova Beach that my super undercarriage wash at the car wash upon our return back flowed through the drain plugs and into the interior. NOPE - absolutely fine - no leak from them.
So I was back to the only thing in recent memory that was different - the windshield. This time I became suspect because of the evenness of the bilateral wetness. What about the windshield/installation would contribute to both sides being wet? Two sides - the left and right molding. I questioned my installer a number of time during the install if the reveal molding on the left and right sides needed replaced. He assured me not. However, this afternoon I tested the wind shield again. This time, I ran a hose from the front of the roof rack down. Remember: I still have the foot wells wide open - so I can see everything. Sure enough, as soon as the hose started running, water was seeping (at an alarming rate) into the interior and pooling on the floor. Over to partznet.com to find me some new molding (left and right) and guess what I see as part of the molding schematic: reveal molding FASTENER (one for each side) with three hole plugs in it. I'll be damned. I'll bet the holes are either unplugged or unfilled on each side. I wonder if the molding fasteners were junked as part of the removal of the old windshield?
2005 Toyota 4Runner Parts - Conicelli Parts Center
Item #10 on the link above.
So Hokie - I wonder if you are missing the same fastener that I am. Your situation sounds identical to mine - just curious: did you go with OEM glass?
Undecided at this time if I want to caulk or if I want to spend $$$ and replace all of the molding.......