1998 Audi Quattro missing and heitation

My 1998 A4 Quqttro has started to miss and hesitate when I give it the gas, my check eng. Light would come on and then go off after awhile, it started out a few months ago just missing when at idle I thought it was the quality of gas so I switched, it has more and more missing and hesitation when first giving it gas and then smooths out and runs fine on the hwy, now it does it all the time when giving it gas, sometimes a lot and sometimes not so much but when it does it a lot the check eng light flashes. So I replaced the plugs and had my friend put the computer on it, it said it was a fuel type code in 3-4 of the cylinders
I replaced the fuel filter with very little change. Where should I go next the fuel pump? And is this a hard thing to replace?