Chad, I have an aluminum floor (exposed w/ no carpet) in my FFR Roadster (cant call it a "Cobra" with Shelby on the litigious prowl). It is going to get scratched up no matter what you do. You can refinish it by sanding (go in only one direction to get a more uniform finish) and while you are building the car you can mask off the floor to help protect it. If you plan on really driving and using your car then some things (like the floor) are going to get dirty, scuffed, and beat up. I have just finished building a car that we built completely, did all the tuning, alignment, bodywork, everything and now I am disassembling the entire car to paint, polish, clean, and detail EVERY part (even sending all fasteners out to be put through a tumbler and then cadmium coated so they are all the same color), and then I will reassemble the whole car for what seems like the tenth (and hopefully final) time. My advice is that unless you are building a show car you should do what you can to protect finishes and keep things clean, but don't sweat the small stuff.
Also Chad you are one of the few guys who are building an SLR so how about an update and some new pics eh?