It should be sticking through the firewall on the passenger side. Typically a black 90 degree rubber elbow turned down. I can't see it in any of the diagrams in the FSM though.
To deal with your initial stink, I have used BG Frigi-fresh, which is an air conditioner air freshener available at some dealerships in my wife's G that gets a funky smell sometime. I will try cleaning the coils next time with some foaming coil cleaner. I used some recently in my truck before installing the cabin air filter and it really freshens things up. You can get it at Home Depot in the area where they stock the window air conditioners. The stuff I used was "A/C Safe" brand and has a lemon scent that's a little overwhelming for the first day or two after you use it. It's about $5 a can.
Heath