Controlling the Auto Smell

Yesterday my neighbour helped me remove the cabin air filter in my Toyota. This is after 
#1 I had read on Wiki-how about changing the air filter without special help. Like I could do it. Pictures were provided.
#2 The article says the filter should be changed every 10,000 miles. Well, that was 110,000+ miles ago for the the last one.
#3 It also said that when you park your car you should push the button to close the air connection with the outside. This would prevent mice & other vermin (I guess snakes) from taking up residence.
Right after I read this article and decided that non-mechanical as I am, I would. change the filter. Except the simple screwdriver tool was a hex type. I do not have that. So, I drove over to my good neighbor's house.
He and his wife were serious pruning one of the large apple trees which is loaded with fruit this year.
But he stopped sawing and took a look at the auto job (with some relief-- those branches are heavy.) I told him that I had just noticed a dead animal smell in the car as I drove over but it could have been my imagination after reading the Wiki-how article.
Whew! When he pulled out the filter we both were overwhelmed with the dead mouse smell. He showed me the hole the little mousey had made in the filter. And looking behind into the engine area we could see a lot of shredded paper. The nest!!
He vacuumed it out. The smell remains today. And there were flies in the car when I went to drive it this afternoon.
Thus the blip today of a household  deodorizing spray. I had opened the hood and sprayed heavily into the space where the nest had been. I hope that sorts it. 
The heavy duty vacuum is supposed to have removed everything...I hope.
From now on I will follow the 10,000 mile directions! The last new filter was installed in 2005. 
Funny how nothing ever lasts!