Rust and water clean up

The area under the fender liner clogged with debris and the cowl leaked into the interior.

So have have the carpet and padding out. I am cleaning out the cowl and fenders.

While I have everything apart I have a few questions:

The inside of the fenders near the rocker panel are just starting to rust.
I am thinking about using a Dremel tool wire cup brush to clean the area up.
What is the recommended product to brush/spray on after I clean up the dirt/rust?

I would like to add some sound proofing while I have the carpet and passing out.
I have looked over many threads on this but my question is fairly specific:
Rather than cover the entire floor with a new layer (not sure that would be effective) Are there areas I should focus on? Example, under the read seat there is not very much insulation. Also in the front footwells.

I have a few workout body plugs, it looks like they are sort of vented, if I replace the plugs should like put some kind of sealer on one or both sides? (these are the plugs in the floor pan under the carpet, not the frame rails.

One more: My fenders have the foam blocks inside the fender at the top of the arch. Should I remove these or cut a part away so they dry out? They are wet with the recent rain.

Thanks!
Anything else I should look at while it is in pieces?

Rust and water clean up