Nome
You need to get your permits in place for certain. Believe it or not, it sounds as if they're being pretty decent about it. You could have been hit with non conformance and code violation fines until such a time as either the permits were in place, and or the garage was restored to the originally permitted condition. Especially that wood stove.
Yes I have heard of garage/car requirement. It doesn't mean that the car has to actually be in the garage. It means that that the garage has not been modified in such a manner as to no longer allow the storage of a car. People will turn garages into spare bedrooms, In-Law apartments, entertainment centers, shops, etc. Thus pre-cluding the use of the garage.
The car issue sounds like a miscommunication. The Bldg inspector should have told the fire marshall that yes, you can still fit a car in the garage unless your modifications would require the removal of physical walls or barriers to fit the car in there.
The wood stove was a big red flag.