Brad Lee, I've been working on something (in a non-arcade related field) using Flash & XML. If you could give me that flash file, I could make it so you could import a .cfg file on the fly into your flash FE that would allow you (or anyone) to make changes to the directories without making changes to the flash itself.
I can control just about everything from directories, to text, to image loading & location, etc, via flash. Names of the roms, their locations, what emulator to use them on, etc.
I could show you a demo of something like this I did for an automotive image company that allows them to load over a hundred thousand images in on the fly, change skins, & text. The product hasn't launched, so I can't post the link, but if you are interested, msg me.