I used POR 15 over the entire floor - easy to paint in, (used a brush), and it turned out great. One quart finished the entire interior, (including rear seat/trunk divider...I think I spent no more than 40 bucks. Just be sure to plug any threaded holes, ie - seat bolt-ins, seatbelt anchors, etc.
depending on your skills and equipment, not to mention if the car is apart enough that spraying wouldn't be a problem... best option would ba an epoxy primer. Good alternative is brushed on por15 as said above.
POR15 really needs a rougher surface than your new floors to adhere best. I think an epoxy primer if you can spray or Eastwood Rust encapsulator. I followed POR15's directions very carefully on my new floors but some would peel off when, for example, I put my tranny crossmember in.
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