Actually, if anyone is interested you can download the necessary conversion software
here.
Keep in mind that this software is Japanese in origin, so a good chunk will not be readable. However, general function should be a no brainer. Keep original folder locations open and files you plan on converted backed up just in case. The software will essentially change your game music into a WAV file, meaning any of your music put in WAV form can be converted back into the BGW file readable by FFXI and will thus replace whatever music was played for the file you replaced.
Keep in mind though, SE kinda beefed up the security and format of their music files post CoP, so anything ToAU related and beyond will be unconvertable, but you should still be able to replace said files with your own as long as they are in WAV format.