I ran into this with my AAR a few months ago......
FIRST remove heater box (as it will be most likely full of seat foam, dead mice, mouse kupa and pee-pee), then drop both fresh air vent assemblies (driver and passenger) (passenger side is part of the heater box), remove the plastic outside air inlet screens beneath the windshield, then duct tape garden hose to shop vac and suck out as much as you can from the top of the fresh air plenum (beneath the winshield)...
then vacuum from the underside of where the vents blow into the cabin, then blast with compressed air from every direction and repeat process several times until you think you have it removed. I then took a bleach/water solution and drowned everything, blew out with compressed air/heat gun about 4 times and most of the stink is gone.
also reach up into the vent openings (under the dash) and get ready to pull loads of mouse house stuff where the vacuum didn't quite reach.
finally drown the entire fresh air plenum (under winshield) and the cavity behind the door hinges with fluid film or some type of rust preventative.
Now you can move onto the heater box restoration, etc.....
this job took me SEVERAL hours/days, and it wasn't easy. i hate what mice do to these cars!!!!!!
i actually had to grind off .050" in the bottom of the heater box assembly, as the urine soaked into the fiberglass! Not Happy! I ended up taking WAY more apart than I initially was thinking as once the mice got in there, they found heaven (nooks, crannies, pockets where nobody will ever find them).