My floor was rusty, but not rusted through. Since I didn't want to replace the floor pans, and they were still structurally solid, I painted them with POR-15 which encapsulates the rust and stops it from spreading. I know your floors are new, but if you can find something like a POR-15 that might make the floors more rust resistant, you'd be ahead of the game. Good luck.
H.
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