I would do a quad core PC using all SATA hard drives, and use one of these:
http://www.newegg.com/Product/Produc...82E16817990003
so you can reboot with a separate system drive set for Pro Tools use. This triple bay unit would also allow you to remove your audio drives when not needed, or the same company makes a single slot version which would be handy for swapping just the system drive. Much like dual boot, but totally separate to avoid any cross contamination and also makes for easy drive cloning(my favorite insurance policy) or you can just save drive images of both versions of system drives.