Hey hey, I think I've hit the jackpot:
LAMEOnJ - The LAME symmetric Java MP3 encoder API
Looks like there's a java api for Lame (which is written in C)... this is just what I was looking for! I only managed to find it after I began researching the indepth mechanics of mp3 file structure.
I'll let you know if I get anywhere with this, Thanks.