I would NOT use silicon on the windshield. They sell a product designed for windshields. Silicone can affect paint in the future.
If the floor is solid under solidly attached sound proofing material leave them both alone. If the soundproofing material is loose it will come with with a little help from a scraper blade.
That floor has crust not just rust. I would sandblast it clean but use a tarp to protect everything except the floor. Sandblasting is guaranteed to put more holes through your floor pan. Sandblasting will not make holes. It will open up holes you do not yet know about which feels the same after looking at the missing metal.
The cheap alternative is to get something like:
https://www.amazon.com/125mm-Strip-Wheel-Removal-Grinder/dp/B07NNWHNY3/ref=sr_1_9?keywords=abrasive+disc+for+drill&qid=1576557670&s=hi&sr=1-9
or
https://www.amazon.com/3M-Paint-Rust-Stripper-Brush/dp/B000BQT4UK/ref=sr_1_22?keywords=abrasive+disc+for+drill&qid=1576557670&s=hi&sr=1-22 <-- [I have used this myself. It works but do not get it near any jagged edges.]
to help remove your rust. Be aware that if you hit an edge of a rusty panel with either of these options you will shred this kind of disc making it unusable or very badly damaged as in pieces of the disc will get cut off.
Your floor needs some welding done. You can use pop rivets instead but that is not a high quality repair. The question is how much new metal is needed. If there are just small pits you can have them mig welded in by making weld dots. A flap disc on a grinder can bring the floor back to almost new status if you are lucky. The larger holes will need new metal panels installed. You may be better off replacing the entire floor pan under the drivers feet. You may not know how bad the metal is until it is cleaned up.
Any good paint should work under the carpet as long as the rust is removed. You could use any rust converting paint including rustoleum for that job.
If the floor is solid under solidly attached sound proofing material leave them both alone. If the soundproofing material is loose it will come with with a little help from a scraper blade.
That floor has crust not just rust. I would sandblast it clean but use a tarp to protect everything except the floor. Sandblasting is guaranteed to put more holes through your floor pan. Sandblasting will not make holes. It will open up holes you do not yet know about which feels the same after looking at the missing metal.
The cheap alternative is to get something like:
https://www.amazon.com/125mm-Strip-Wheel-Removal-Grinder/dp/B07NNWHNY3/ref=sr_1_9?keywords=abrasive+disc+for+drill&qid=1576557670&s=hi&sr=1-9
or
https://www.amazon.com/3M-Paint-Rust-Stripper-Brush/dp/B000BQT4UK/ref=sr_1_22?keywords=abrasive+disc+for+drill&qid=1576557670&s=hi&sr=1-22 <-- [I have used this myself. It works but do not get it near any jagged edges.]
to help remove your rust. Be aware that if you hit an edge of a rusty panel with either of these options you will shred this kind of disc making it unusable or very badly damaged as in pieces of the disc will get cut off.
Your floor needs some welding done. You can use pop rivets instead but that is not a high quality repair. The question is how much new metal is needed. If there are just small pits you can have them mig welded in by making weld dots. A flap disc on a grinder can bring the floor back to almost new status if you are lucky. The larger holes will need new metal panels installed. You may be better off replacing the entire floor pan under the drivers feet. You may not know how bad the metal is until it is cleaned up.
Any good paint should work under the carpet as long as the rust is removed. You could use any rust converting paint including rustoleum for that job.