do you smoke?
I know "what the hell does that have to do with it?" right???
I've found that when I have the window cracked open to ash my smoke that it will suck fumes in from either under the jeep or around the back door/window.
Also, make sure your plate above your trans (between the cab and the trans that your shifter goes through) is sealed up good. And, make sure your shift boot did'nt get a tear in it