1969 AMC Javelin Interior Repair

New to the forum, so hopefully I am posting this in the proper section.

I recently purchased an all original 1969 390 AMC Javelin SST painted in the original big bad blue color. This is a pretty rare care, and it needs some body work, primarily above the rear wheel wells where there is a considerable amount of rust. I am going to end up getting the entire car repainted and all of the body fixed sometime in 2019.

My question is this...  I pulled up the carpet last week, and found what look to be decent floors minus the dirt and surface rust accumulated over the years (I pulled out about 5 dead rats when I cleaned out the car). What should I do about this surface rust? Should I remove it all and primer/paint it in a black color to protect it, or should I just wait and have the pros handle it when they repaint the car the original blue? I obviously want to protect the floor of the car from further rust, but I also don't want to do something stupid and devalue the car, as this vehicle seems to be completely original. Any thoughts on this as you will not even see the paint when the floors are covered with carpet later on? 

Vacuum all the loose stuff, take a rag and soak it in vinegar, lay it on the rust spot, cover with wax paper and let it sit for a couple of days.

Rinse off and dry the now bare metal, prime immediately. If there is still rust, then repeat.

Seen a whole car done like this to strip rust - works quite well.