RUST? Where? that's nothing. I had complete holes in my floors. Thought I was going to lose a kid through them rolling down the road. Take a wire wheel or flap disk to them to get rid of the rust and some rust converter. If it is too thin or rusted through at all just cut it out and patch it with some sheet metal. If you can't weld or don't have anyone to do it for you just slap the patch down with some self tapping sheet metal screws or rivets and make sure you seal it all up. Then bedliner over top of it and you're good.
If you ever need full replacement floor pans check out classic 2 current. I think I paid $70 - $80 for the fronts and I forget on the rears... good luck.
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