Now that I'm using Litestep, for some reason IconPackager won't change my system icons. I'm thinking this is because explorer.exe isn't running as the main shell? Does anyone have a solution to this problem?

You can use this program http://www.users.on.net/johnson/resourcehacker/
You have to edit the shell32.dll by hand
And then I used replacer to save the file when I was done.
http://www3.telus.net/_/replacer/