If there is something dead in the vents and I cannot find it. Could it possilby be from the unit itself? After I checked the vents I dissasembeld some of the unit the vent box and checked inside the heat exchanger and smell was in there. I also checked the return and changed the filter. If the mouse died inside the heat exchanger, how long will the smell last? I bought some fragrance for the filter from home depot, in hopes of covering the smell? Should I call in a repairman as this unit is under my homewarranty?

Before you call you "Home Warranty" you had better read about the coverage. I am not sure that they would cover an odor that was not a danger to you.