However there seems to be a million and one different standoffs on the chassis which are stopping me from installing the motherboard as they are pushing against the bottom of the heatsink retention bracket. They don't seem to be detachable either so what's the best way to remove them?
use the tool that came with the chassis, they are a nut/bolt pair.
Unfortunately this chassis didn't come with a tool (I ordered a 512-200b at the same time and that did). Also, the standoffs seem to be permantly attached to the chassis (the area that sticks out is round so can't use pliers etc). Should i try and find something to cut them with?
The more I look into this the more I don't think this chassis was really built for this motherboard. For example it comes with a IDE DVD rom and the motherboard doesn't even have an IDE connector! Not sure why Supermicro listed it as optimized?