I'd suggest you build your system and live with it for a while before doing any hacking. I'm the happy owner of a PC-65b, and it's just too nice to hack up with unneccessary "mods".
Most of the things I've done over the 8 months I've had this case were performance-oriented, such as cutting out the rear grill for better exhaust air flow, and opening up the "louvers" on the top blowhole .(almost a 50% increase in airflow!)
I did originally stealth the CD drives, but I recently went to the factory "stealth" panel on the CD reader, as I got one at a great price. I'd suggest using those vs. home-made on a new build, they look great and work very well!