Hey, just an fyi. Rain was still coming in through the sunroof after I adjusted the antenna wire.. It just needs to be sealed with some superglue where the lining around the glass meets right in the center.
The leak I'm referring to is coming just about where the "1" is. Right in the center where the rubber seal meets.
I know for certain water was coming down the antenna too though. I'll get some pictures up here for you shortly.
Here are some pics from 4runners.org that might be able to help you out.
Remove the Wheel well liner by first removing the fender flares:
If your antenna wire is running straight into the the hole, chances are the water was running down it into your passengerside floor.
Seen here are the holes, but for me I had an aftermarket antenna and the wire was actually running into the top hole.
I pulled some of the wire out of the cabin and made it go around the bracket for the power antenna. I then zip tied it to the bracket so it wouldn't move. The water then would not be able to run up the wire into the cabin.
The bracket can be seen here as well as the holes. The bracket is on the right with the nut in it.
Hopefully this helps. Let me know if you need any more clarification.