I like the idea of moving the motherboard away of the tiny case. I might try after I get a bit more time.
I am guessing that because my server has hardware RAID, I will have to cut the drive bays out (which is essentially a huge chunk of metal) and smash it into a large case... or leave it outside. I guess I will look for a nice large case, so instead of having to shove in 40mm fans that go at 25000 RPM into a already-cramped 2U case, I could get a nice, large, 120mm fan that doesn't make any noise sitting right next to all the heat sinks.
But then again, to sufficiently cool the computer and to prevent warm air brewing inside the case, I might have to carve a few holes for a couple more case fans.
The server I have is pretty large... would it be wise to get something big as 4U and spaciously put everything in?