Even though this originates from trying to change the appearance, I feel it fits better under Hacks than Themes. After rooting, installing the custom ROM, busybox, the transparent notification bar/shade, and custom boot animation, I decided to try to change some more things. Drunk on noob-juice, I thought that I could unpack framework-res, change the colors on some of the icons, and repack it and move back to the Droid.
My first clue should have been my icon was a different size than the original. After installing everything I rebooted only to find my phone stuck at the white M. Long story short, thanks to the SirPsychos custom rom, I was able to adb the original framework back into /system/framework and return the phone to working order.
Moral of the story: even if you think you know what you are doing you probably don't. If you are a fool and don't let minor details like that bother you make sure to install a ROM so you can fix what you will inevitably botch. I'm happy to say this was nothing more than a learning experience and I'm glad I was able to sort it out without having to plead for help.