You could do all this stuff by hand, but as far as I know tehre isnt much room in that case for much modding. The whole ssytem is deesigned for maximum airflow so tampering with the design
1) will void the warranty
2) may cause permanent component damage due to a disruption in the system's overall cooling mechanism.
Plus, its so beautiful, why tamper with it like those PC case modders do with theirs? We do things differently in the Mac world. Low level case mods like windows and lights really just seem childish. If youre going to mod an Apple, its gotta be big for it to look good.