Is it possible to customize the in-game soundtrack? I tried just throwing some mp3's in the Music folder, but it looks like they have to be named according to the levels. Any way around this? Or, any easy method involving bulk renaming?
Nothing against the included rock music, but it would be pretty sweet to frag to Cut Copy and Stevie Wonder. :D

Yeah, I've done that. It works, it just loses the immersion of the music syncing with the action.

If there isn't any map editor for the game then You must change names and rewrite original files I am afraid.

Assuming they are sequentially named otherwise you may as well do them 1 at a time, you can rename a large number just in windows explorer.
Hold control and select the files you wish to rename. They have to be of the same format so .mp3 or whatever painkiller uses. Rename the first file and put the INITIAL desired number in PARENTHESIS,
so your song would go from say "song name" to "painkillerlevel(1)"(of course use the correct names that painkiller already uses), the parenthesis commands explorer to rename the rest of the selected files in order.
I would also backup the painkiller music incase you decide to go back to it saving you a reinstall.

Unfortunately this won't work (I think). The files aren't sequentially numbered, but named after the levels which play them (C1L2_Atrium_Complex_&_C3L3_Military_Base_Fight.mp3, C3L2_Factory_Music_01.mp3, C6L3_Lab_Fight.mp3, etc.).
What I really need is some way to export a directory's filenames, and then rename other files to the entries in that list. I've been screwing around with various bulk renamers, but I can't find one that performs this function. Surely there must be one.....

what, manually is too good for you?

Actually, I've found that by focusing on the nuances of the original soundtrack, my appreciation grows to surpass my malcontent. What's the sound of one hand, etc.