You could try running a bash script to rename the roms. I don’t know how to do that myself but try google (http://bfy.tw/rVb)

Regards the gamelist.xml files, the simplest solution may be to insert your SD card into your desktop and use the search and replace function on a text editor.

Either way, make sure you back up your romset and gamelist.xml before you start. It may also be worthwhile trying your bash script on a subset of roms.