Any ideas as to why my car runs and idles rough (looks like it has a CAM but its stock)

I have a 95 5.0 mustang gt. It has been giving me problems recently. Once it gets warmed up, the car idles and runs extremely rough, almost as if it has a cam in it, even though the car is completely stock for the most part. When the car is warmed up and you go to give it gas, there is an intermittent shutter and usually hesitation. There is even times when the car shakes and will not let you go over 2500 rpm. Then if you let off and punch it, it will temporarily clear up, only to do it again a minute or so later. I have also noticed that under hard acceleration that it jerks and the tach will jump. We have deleted the cats, added flowmaster dual exhaust, replaced the distributor and cap, ignition, done a vacuum test, replaced plugs and plug wires, replaced throttle body, replaced tranny fluid and filter, and replaced all of the O2 sensors; just to name a few things. Hooked up the obd1 reader and it said bank 1 ran lean. The car is getting to be a pain. I love it wholeheartedly and just want to get her back on the road again running well.