Cobra Dragsters Problems

Hey guys Im new and need a little advice. Some background on the bike is, its stock except for the new Cobra Dragsters and has about 2500 miles on it. I installed the new pipes installation was pretty simple only thing i did was route the o2 sensor pigtail a lil different so it was totally out of sight. I rode it to work and she sounded awesome but under load at steady throttle it will sometime hiccup, Im assuming the pipes are just a lil much for the stock mapping. I ordered a Cobra PowerPro auto fuel tuner and will be putting it on later this week. You guys cant think of anything else that could cause this outta the blue. Also anyone familiar with the powerpro tuner. Im also installing a hypercharger intake.