Hi John,
You will probably do well to start with the source code for Jasper (the Java Atari ST emulator). I forget the URL but Google will find it.
It has a great Java 68k emulator in it... as for the custom chips... their functions are pretty easy to emulate, but Good luck with all the timing crap that goes with it...
-EDIT- Ok here is the URL for that Java ST emulator... I'm too nice... thats my problem ;-)
http://www.atari-st.lovely.net/