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Yes, looks like the top part of the windshield side trim is gone. Odd, was it cut off at some point? Is the trim on the side of the windshield still there? The trim should start at the cowling and go about halfway back to the roof rail, in one continuous piece. My guess is that, if the lower part is left at all, it was attached with screws that are leaking, instead of the proper rivets. Remove the screws and replace with the proper plastic coated rivets. There are how-to guides for this on MUD. I got mine on ebay in a box of 10, enough to do both sides with a couple spares.. Coat them with some 3M body sealer (VERY sticky stuff) before you put them in to make sure you get a good seal. Also check that the bolts for the roof rails weren't messed with. Don't worry about the bolts under the rack, but I think there is still one bolt in front of the rack, in the drain channel, if I remember right? Make sure that one is tight and sealed up OK, too.
We need another picture, that gap is usually filled by upper portion of the trim strip that is riveted to the a-pillar. It's hard to tell from the photo, but it looks like that entire piece is missing.
This old thread of mine may have some photos that help: Couldn't take it any longer, it was time to take a look under my windshield trim
Look at the photo in post #14, it shows the black trim strip you may be missing, it runs the entire length of the a pillar.
Here's another http://i.imgur.com/33YwiXY.jpg
Oh my, someone did you a disservice on that windshield replacement. You're missing the a-pillar trim on both sides which isn't helping your water issues since there are 4 holes in each a-pillar where that trim is fastened to the car.
I don't think there is a way to make this right without pulling the windshield and having it re-installed correctly with all the necessary trim.
Aw man. Yeah the windshield trim looks atrocious.
Sorry, hopefully you can get it sorted out without too much pain. I'd try to find someone that's familiar with Cruisers or LXs, maybe ask the Toyota or Lexus dealer who they use for glass replacement. Glass techs typically are carrying around rivets so often times they use whatever they can find in the truck to secure the molding to the a-pillar which doesn't always yield great results.
Alright, thanks for the help.
No problem, per the attached, you'll need part #2 for both sides and part #3 for both sides (this is for an '06, your part numbers may be different).
View attachment 1453697
That trim has nothing to do with the leak.
The missing trim sure isn't helping matters, but you bring up a good point. The entire windshield install is suspect, simply slapping the proper molding on the a-pillar isn't going fix anything if the glass isn't properly set or there is significant rust in the frame.