help with hesitation / miss

I have a 98 GT 4.6L w/PI heads & intake, accufab 75mm TB & plenum, Ford headers, MAC mass air meter but it is only a cold air intake using stock sensor and 3.73 gears. When I am in 5th(or any gear while at low RPMs) at about 1500-2000 RPMs and I step on it I get a miss or hesitation until RPMs get up a little, also when going about 80-85 MPH and step on it the engine will miss while it is getting up to speed. What do I start with to correct? Thanks in advance for any help.

This is a rebuilt motor that I have put about 1200 miles on so far. I did the head swap kit so the plugs only have the 1200 miles on them, as far as fuel filter goes I'm not sure how long it's been.