I cut pieces of threaded rod and used those long nuts,(I dont know what they are called) but they are about 1 1/2 long themselves. If I remeber correctly I had to re tap one end. I think maybe metric on the Konis. As it worked out the threaded rod only sticks out far enough to go through the shock perch and take a nut and washer. I was concerned about the rod strength. Well most of its lencth is encased in the 1 1/2 nut and its done tight to the shock rod. I have put a couple thousand miles on the Konis and no issues. I would be glad to take a picture if you like.
It was about six years ago when I checked into the same thing only with the Konis. The Cougar rear are longer. You would have to hit the bumps pretty hard to do any damage to the shocks I imagine. But I would think Koni and Bilstein or KYB either for that matter know what they are doing. If the Cougar is longer I think it would be better to get the shock length right. If the shocks are for Mustang just take into consideration how much you lower it and fix the shocks. The nuts and threaded rod only cost a few bucks and its a quick fix.
Called bilstein today, they said they make them for rcd and can't give me no info on them. I went to rcd website and they say the backs are the same as the mustangs. I just can't find info about why 66 and 67they are different