Well, you did 2 things to your rifle after you got good groups; you cleaned it and you installed a hammer extension. It would seem that one of these things could be to blame for your accuracy problems.
Each to his own, but I have all sorts of scoped Encore barrels with various scopes including Leupold handgun scopes, have had the banned guy's trigger jobs and have never had to resort to a hammer extension on any of them. If I were you, I would remove the hammer extension and learn to cock the hammer without it.
Exactly how are you cleaning the barrel? If you're cleaning the same way as you clean your muzzle loader barrel and haven't ruined that one, then how you clean probably isn't the cause of your problem.