ARGH. I really wanted to do something like this. Well, I just wanted to put my components in the G5 case... It really does look nice.
Anyways... If you could make it look good, I'd say go with a side window after you get the cables neatly managed and a full water loop in there. I think that would look pretty nifty.
I also don't think you should paint it... possibly powdercoat it if the scratches are absolutely unbearable.
I'm really looking forward to how this will come out.