Started misfiring, changed plugs and fuel filter with no results, what could it be?

don't know which engine you have,but one of them has a coil for each cylinder,and one has a coil pack with wires. if it has wires,how long have they been on,and have you checked them.the other 3.0L has a coil for each cylinder. if it has the cop coils,you could start it and unplug the electrical connector on one coil at a time to see if the engine idle changes,if it does change that coil is good.plug it back up and move to the next one.if you unplug one and the engine does not change,that coil is bad.