Ive been searching this site for ages trying to find the problem with my TJ wagon. In even the lightest rain water would make its way in and wetting the front and back carpet coming in from the area behind quarter panel. I took of the quarter panel which was piece of cake and silicone sealed all grommets and anything else that might leak but it still leaked. Where the water goes down the side of the wheel arch there is a small channel which you can not get to unless breaking some welds which I did not want to do so I put a lot of silicone down it and with a small flat bit of wood was able to rub/smooth it as best as I could reach. So after 4 days of trying everything, no leaks and can finally park car outside. Thought I would post my problem hoping can help others with this problem.

I would strongly advise you remove all the silicone as soon as you can and replace with a urethane based sealant as silicone is very acidic and in a matter of a short time you may find you have more rust than you can poke a stick through.

The area that often is starting to let go in these older cars is around the bonnet hinge, have seen this a few times. Other problem is the cover for the cabin air intake, often needs to be sealed as the foam seal has let go over the years

Thanks I'll take a look at what type i used it was a metal type silicone also after another huge rain once again still tiny bit of water made its why back in. So back to square one but notice the rubber seal along the side of windscreen looked a little warn and was wet behind it so dryed it and sealed that to poured water again today and no leaks fingers crossed this works. Now i know why car smelt bit funny when we brought it.

i feel your pain. i had this in my car for ages. drove me nuts....took the front fender off many times to ensure i sealed everything properly. Finally got it sealed after months. Heres what i did:

removed front fender, sealed everything i thought i could using sikaflex automotive sealant(comes in black or white, got it from bunnings).Let it dry, sprayed water with a hose, i used the shower setting on the hose, carefullly sprayed small sections of the passenger area, Started low then worked my way up to the screen.

Found it only leaked at the very bottom of the windscreen. At which point i thought was the windscreen.....but it was not. I then removed the passenger side A pillar and the little cutout for the in dash tweeter, put the hose on the front of the windscreen and set it to keep spraying while on the inside i used a torch and aimed it down the hole in the dash that the A pillar sits in. Aimed it right to the edge where the windscreen meets the metal.

I saw water seep through the seal in the corner( a bit hard to describe but its a seal a bit like a hard putty type they use). basically it was leaking right from the corner of the car. To fix i sealed on the outside, near the windscreen area, and a little bit under the rubber strip that extends a little bit from the windscreen.

As Madmagna said the hinges could be leaking. I also sealed all around the bonnet hinge as well as the cover for the cabin air intake. Also replaced the plastic cover, they are $20 for each side from mitsubishi.

I had the same problem I went to a mechanic he said the heater core that was lies
I had a tiny rust hole above the fire wall hole so water was just dripping through under that water tunnel thing under the window so just gotta take the front quater panel off and fix that little rust hole and all done