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The one thing you will struggle with is fitting the mugen with the motherboard inside the case. The fans around the HSF give you very little room to get to the base of the HSF on all sides so I would fit the HSF outside with the mobo out but I always do that with the ninja anyway to make sure the bloomin thing is on right.
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Staying at the bottom of the case, if you have a modular PSU try to figure out what cables you will want to use before you start buidling and then fit them before it goes in. The way I fit the power supply is to follow its guide in the manual but fit from the motherboard tray side with all the cables facing out (since they will all go behind the mobo tray eventually).
Corsair Modular PSU for the win :p, but thanks for the advice about choosing and figuring out which cables I will need etc, I just hope there is enough length in them to reach all my bits and bobs in the system.