Jake,
Littleben is right, especially since that riser already has the threaded hole for an elevated rest anyway. I would say a flipper style rest would be best but its just a matter of preference.
If you are absolutely stuck on shooting it off of the shelf, you will need to build the shelf back to center with something, be it a machined block of aluminum bolted to that same hole, or something carved from wood, or even sculpted/carved out of bondo or something. Heck, if all you want is function, you could bolt a stack of washers to it to bring it out to center. That may look sort of trailer park though.
As far as measuring center, use the center of the handle for reference. It's already right there close to where you will be working anyway.