I had a similar problem on my CB750K3, a PO (the bastard!) cut a large part of the threaded portion off the end of each stud on my upper shock mounts, so I cut them both flush with the shock mount itself, drilled (and drilled and drilled, that steel is HARD!) the mountiing boss out and tapped it for 10 x 1.25mm thread (you can't buy threaded rod in that size apparently) instead of using a couple of 10x1.25mm bolts with their heads cut off I just threaded the bolts straight in with the grab rail and a couple of stainless plain and spring washers to stop them from winding out.
They look really good, and honda should have done it from new, because fitting new shocks is now a piece of piss! All I do is line up the clevis mounts on the swingarm, loosely thread that bolt in, then slide the top shock body mount over the mounting boss on the frame, then fit the grab rail, thread in the bolts etc, tighten it all up and it's done, no swearing or cussing required. Cheers, Terry.