So I tried to completely remove the Windows UI with ObjectDock and have successfully been able to do it on my Windows XP machine with little to no problems, but running it on Vista 64, I get constant freezes which I can only solve by restarting/logging out. I can't even kill the process in the Task Manager because everything freezes.
It seems after removing the systray dock I had, I no longer got any freezes. I'll wait and see though.