Once you do that, kill the process in Activity Monitor and relaunch ShiftIt (if it still exists on your computer). If it doesn't exist then restarting your computer should kill the process and it won't have any place to restart from since you deleted it.
As for compiling-- check your project settings and ensure that you've got all of the needed SDKs and you're compiling for the right architecture. Other than that, I don't really have time to help further troubleshoot right now. Perhaps someone will chime in.
-Chris
As for opening the preferences-- once you get a newer version from Github (e.g., 1.5) you can launch open the pref pane when the icon is hidden by simply launching ShiftIt for a second time when it is already running.
-Chris
Have you tried restarting your computer?
-Chris
-Chris