I had the same problem. On the right side the bottom of the backrest that goes on to the cam was hitting the top of the shock just enough to stop it from going all the way in an locking. I was upset that my old backrest would not work with my new bike even though the dealer told me it would. So I used my bench top grinder and removed just enough material off the bottom where it was hitting the shock. Backrest goes on easy and locks. The next day I walked into my local aftermarket harley shop and the mechanic was doing the same thing to a new backrest to install it.
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Are you sure your right rear shock wasn't upside down? Many came from the factory this way.
Sure did, I helped a friend install his docking hardware for a sissy bar and luggage rack. I had my stuff installed at the dealership before I picked the bike up new with some other stuff I wanted added, so I don't know if mine was that way as well. His had one shock right side up, one shock upside down. Rode back to the dealership and said hey can you fix this. Half an hour later problem solved both shock right side up, and no labor charge since is was a factory beer Friday. Cheeseheads drink a lot