The best I was able to do was to wash it with a baking soda mix. Then I left a shallow pan of baking soda under each side of the back seat for a week or so. It pretty well killed it except for really hot days with the windows closed up.
Don't forget the headliner. I did a 49 Packard and when I took down the headliner, there was about 10 pounds of mouse nest that came down with it. They get behind the kick panels and up under the seats too, where there are all kinds of great mouse nest materials. I would strip the interior completely down to the sheet metal, clean it real well and let it sit for a while before putting anything back in.
i went through this in the late 70's . i ended up with a sinus infection that moved into my lungs. took several months to get over. all caused by blowing out an old barn find. mice are nasty creatures. doc said an infection like this can cause serious damage to the lungs. anyway water is the best way to clean out old cars anyway. gets all the dirt out.