In cases like this I have used eastwoods "metal ready" and I'm pleased with it. I assume there's no paint on your floors. After that treatment I spray with Southern Polyurethanes epoxy primer. Actually I'm doing mine now After I weld in a patch panel. The "metal ready" will remove the rust discoloration in 15 miutes and leave a phosphate coating to help prevent future rust.
Just my $.02
Keith