95 mustang gt running rough

5.0, car runs rough like its cutting out some during lower rpm, after i give it gas it smooths out and runs great. If it shifts into higher gear while going too slow it really does it. It has a new fuel filter and fuel pump. Mild upgrades include cold air intake, B-Cam, shorty headers with x pipe. Anyone have any ideas where to start with this or have experienced something close to this all help and advice will be greatly appreciated.
 
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