Did you plug in the tune before you started the truck? If so then you might need a crank relearn. Or another possibilty is if you didnt pull your plugs out when installing them you might have smacked a plug with the header and cracked it? That happend to me and it drove fine everywhere except light throttle where it would stumble which I had no idea what it was at first because I didnt realize I had a cracked plug. Maybe one of your plug wires isnt on all the way?