Some places you might concider cutting on the mobo tray would be
1. right behind the front audio/usb/firewire wires so you can run them behind the mobo tray.. OR move it somewhere else.
2. hole for the 24 pin, PCIe, 4/8 pin and SATA cables.
You should concider replacing the fans with some Yate Loons - quieter.. I just picked up 3 or 4 of them the other day at
www.performance-pcs.comLook up some plastic die. You can find it at most auto parts stores I believe, AAANNDD you should be able to die those ugly purple drive clips black, or whatever color you want them.
To increase airflow, you COULD rebuild the HDD tray.. Less restrictions = better cooling. If you're not going to have but 1 or 2 HDD's in there, you can ghetto mount them on the bottom of the case and open up that little section f the fron of the case for some quality air flow.
Keep us posted.. txt me if you have any quick questions