Both of the pipes did that, shortly after the install. I tried some of that "blue job" or something like that, to remove the bluing. I just didnt work on the front pipe as much. The HD dealer did a remap for the pipes/KN, so I wouldn't think its a fueling problem. It runs flawlessly.
I might be interested in taking a look at it. My wife just got her license and wants a Nightster. Let me speak with her tonight and see what she thinks. I live in Bolingbrook which is about 150 miles from you. Do you have the stock parts for it?? She will not be a big fan of the apes on it.