After reading through the forums more I came across this post by pappukanghi:http://www.kessels.com/forum/index.php?topic=1089.0
After doing some research on the forums it looks like it will be hard to do what I mentioned above until version 4 comes out.
Until then I am going to use pappukanghi's batch file and list and see how it works for me. It looks like it does what I am looking for. Hopefully =)
Though if anyone still has any suggestions please feel free to reply. JkDefrag is awesome!