1992f150raptor

i recently installed a 3 in exhaust with no cats and a flowmaster muffler, since then my eng runs rough, is it possible to have to little back pressure with a speed density fuel injection(ie to fix it I would have to increase the fuel injectors or change the comp tune to make up for the eng breathing more, I have checked for vaccume leaks and for plug and wire problems, please give me some advice, maybe someone has run in this before