I may be way off, because this would not pertain to the smell issue. But I had a problem with my 99 last summer when trying to use the AC. Only hot air came out. Apparently the blend door actuator needed to be replaced. This is about a $6.00 piece that moves one dirrection to let hot air in and the other to let cooler air in. I was told they just eventually wear out. Unfortunatly in my year/model this piece is very hard to get to and cost me $1,600 in labor.
Again probably not your problem, but thought it worth mentioning. | 
