My 1st idea to put MB upside-down on the top of the case.
And put the DVD at an angle. The RAM would be in the way. Could do it without the DVD though.
Idea to put all wires inside. Power/reset buttons too close to CPU.
A mod I did back in the day to my Nintendo(also why I had to get one from eBay). Wired a 1/8 inch jack to the Reset button so I could reset from far away. It was mainly for the game "Nobunaga's Ambition". And there is the black tape over the LED, so I could pause it and my parents wouldn't know it was on.