Motorcycle Repair: S&S 113ci motor troubles, crane ignition, johnny p

Question
I have a s&s 113ci motor in my custom softtail. I have 500miles on it. Sent it to the local v-twin shop for oil/general break-in tune-up. It runs great. Just out of my easy break-in miles. They call back to say at 4000rpm it falls flat. I have a crane ignition system/vance&hinds long shots/superG carb. They say the rev limiter is set good and ignition is good. Could it be in the carb? I did notice some black residue on the ends of my pipes. What should I look at first-second-third? Any help would be appreciated. Thanks

Answer
get rid of the Vance and Hines long shots. they are KILLING your HorsePower!!!!!!!!!!!!!!!!!
Cycle Shack PDH 2" duel stepped headers are the best on the market.  Johnny  P.S. It is the exhaust system. You will never ever ever get the bike tuned correctly with the long shots.