The exposed aluminium will be oxidised to form Aluminium Oxide. It will not really discolour. However, instead of being shiny it will become a dull grey colour.
I would not advise sanding the whole case unless you plan to paint it. The problem with sanding it is that you remove the anodising. The anodised layer is much tougher than aluminium oxide. If you remove it the case will be scratched far more easily. Apple anodised it for a reason. In saying that, sanding small, non-visible areas should be OK.
I have seen some cool polished mod.s where all the coating was sanded off, polished and then lacquered to protect it. Looks amazing, but is high maintenance - every fingerprint shows up.
Ok peeps, its been awhile but life got in the way, a small update, so over the last few days have managed to get the motherboard in place, it's in my garage setting.
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