It looks like the problem is originating under the dash, as you can see where water has been running/seeping down...like you said the clutch, so stop that first, then look at using naval jelly or this
Eastwood Rust Treatment: Rust Removal, Prevention & Protective Gear then use a wire brush wheel on a grinder, drill or whatever you have to clean it up...paint it with
Rust Converter - Eastwood Rust Treatment & Prevention Products scuff it and paint it with regular paint, ...wait a while before you try the bedliner stuff, reason being, if you miss a little rust, it will keep on rusting under the coating, you won't know untill it is too late...
