I actually sold that Mac Pro in my sig, I am thinking about getting a new one. I might just get one of those custom dual 8 core 3.33GHz machines off eBay. This guy is adding the chips to the 8-core systems making them duals running at 3.33GHz. Pretty damn cool, but pretty damn expensive too.
Ah, OK.
Then if you're going with a 2009 system, you need to order an Octad if you want the second processor (it's technically possible to do with a Quad model, but all the parts will make it unfeasible financially speaking).
So get the second CPU when you buy (clock speed and source is up to you).
BTW, if it has to go back to Apple for repairs, you'd need the original processors (and any other equipment that's been upgraded from the system Apple originally sold). Add-ons are supposed to be removed before returning it to Apple for repair/replacement (system returned to original hardware prior to any work being performed). If you don't do this, there's a seriousl chance you're upgraded parts will disappear (others have had this happen).
Just a warning to check into these details from the seller if you go that route.