Where does the exhaust dump out on your 4runner? When it dumped out the side of my old one, i never got any fumes. As soon as I got rid of the tail pipe and just had a turn down it was horrible. On my new runner I have just a muffler and a tip on it that is slanted and its not toooooo bad but it still sucks.
EDIT: On a 2005 that I was driving around the fumes were actually pretty horrible. It was all stock too