Good evening everyone
I have a 1980 Gran Fury squad car. It has sat since 1989 and the passenger side window was broken out. Well while it was stored in a garage and there was a mouse infestation inside.

I have vacuum the interior and ran a ozone machine for hours and it still smells brutal inside
I'm planning to gut and clean everything in the interior. The seats need to be reupholstered so they will get new foam and fabric. My question is what can I do while I am in there?

Any suggestions are greatly appreciated

Find an air ionizer. The ozone created by the ionizer will kill the smell and any cooties. If you are working on it beforehand, wear gloves and at least an N95 respirator. Think Hantavirus and some other wonderful things. Bad news. Also you could bleach bomb it.

My GTX sat from 1982 until I bought it - same issue. Mice made a hotel in the headliner.
I replaced both the headliner and carpet, washed the vinyl seats and trim panels three times with Dawn dish soap and a soft bristle brush. Let them set out in the sun until dry each time. Soaked the backsides each time with Fabreze.

Spray dyed the plastic kick panels and seat back.

Smells like a new car.

Side note. I had a rental that had cats and dogs that messed the basement up. I tried everything to get rid of the stench.

Tried for weeks. Vinegar and baking soda in two days and the stench was gone.

Burn the carpet and seat upholstery. Wash everything else with Hydrogen Peroxide. The first aid stuff isn't strong enough. Get it from a Beauty Salon supplier. In a pinch you can try Oxyclean type cleaners. You have to oxidize the pee to get rid of the smell

until you clean all the surfaces and either replace or use a shampooer/carpet extractor on the seats and carpet the smell will always be there. SInce you said you are replacing that stuff anyway tear it out and the smell will go away.

Dont overlook the heater box and vents, ducts, they love those.

I had a similar issue with a GM car. I gutted the interior and used my hot water pressure washer in the inside shell. followed that up with a coat of rustoleum flat back on the inside shell. Brushed it on. All the plastic garnish moldings have been redyed. The dash can be an issue also as they pee everywhere in and on top of everything. Upholstry is all new. I think i got it but it was a lot of work.and cost

https://www.nucalgon.com/products/indoor-air-quality/clenair-original-odor-neutralizer/

I have customers that order this stuff by the case for mouse and dampness odors in buildings that have been vacant for awhile.

Because a GM stunk when it left the dealer.

Another, useful, well thought out and intelligent reply

before i started my machinist career, i worked at a house trailer plant for a few months.
this was at the time when 14 wide by 70 feet long trailers were no allowed on Pennsylvania roads, but the place was building that size trailer exclusively, as it was expected the law would change at any time. [and it eventually did]
a person wouldn't believe what those idiotic workers put in the walls of those trailers to make them stink, and be a hard thing for the obnoxious smell[s] to be located...........
i'm glad that stint only lasted a few months ! my machinist career was MUCH more rewarding.

I included that fact understanding GM used some different techniques in how the inner shell was finished that wouldn't apply to a Mopar.

Have a great day !