Floor prep/rust prevention before sound mat

I have pulled the interior out to get ready for a 4 speed swap and putting in sound mat. The floors overall are in pretty good shape, but there are little spots of surface rust.

I want to get ahead of it, especially before covering with sound mat etc.

how best to prep and protect? Someone recommended I wet sand and the use a rust paint?

it also looks like there is some kind of caulking or putty on seams - it just pulls right off, what is/what should I replace that with?...

Floor prep/rust prevention before sound mat
Author: Cmuller0420