Why do you want it to run as root? It really shouldn't. Try hacking my installer, it should only be necessary to change the "fah_dir" variable in a few places to make it use the folder of your choice. As for running as root, I went through a lot of trouble to make sure it doesn't need to run as root. You would need to hack the foldingathome init script and the reconfigure script. The really quick and dirty way is to use su (read the man page).
You can give it a command line option to finish the current unit and send and quit: '-oneunit'. If using my installer, you would this option to the /etc/default/foldingathome file and restart.
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