Not everyone has the time for this kind of thing, but my preference is to buy a new SATA drive, and do a from-the-ground-up install of the OS, and FCP and everything else.
Keeping the old installation handy incase things go south. That's never happened but it's also been good to keep a reference list form the old applications folder to track the myriad of little utility programs I have installed over the past year or so.
Before I had one of those SATA docks I would just pop the new drive into the MacPro and leave it there. Over the next few days it will slowly become the default startup disk until everything is installed and proven to work.
I think I run a pretty bug free system and, with no evidence to back me up other than anecdotal experience, I would like to say it's because I always do a fresh install.
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Sleeplings, AWAKE!