Last year i had Kooks LT headers and Xpipe fitted and with my SCT Xcal tuner went to a place who fitted the pipes then used the tuner and a dyno to get me from 268-301RWHP. I feel your pain as when i first got the tuner and started to use it on my own it didnt work out, probably because i didnt have any experiance using it. Not really much help i know but thought i would mention having it dyno tuned by someone might not be a bad idea. FYI it cost me $250 for the dyno tune. I have before and after videos if your interested.
2007 Mustang GT Roush Stage 1 w/2.6 Kenne Bell, Kooks LT & X-pipe 430RWHP