Over Asked Probaly But Need Help?

Okay what I Have.... 1996 Mustang Gt 4.6 2v 5 sp roughly 80,000 miles on it ,Bassani on road x-pipe,short throw shifter, 3.73 gears ( i think),and of coarse flows,....I have had the car for a while now and who owned it before me was opposite on my mentality of cars they wanted looks before performance (hence no real performance work besides gears...but plenty of cosemetics, cobra wheels,saleen wing,cobra hood tinted windows,)...Now my problem a while back i noticed on heavy acceleration a little skip but jus a little would occur above the 3k rpm mark, but after time it has got worse where it is a bad skip (and i mean performance detrifying) anytime i get over 30% throttle but any less and its like theres no problem runs fine and the check engine light isnt comming on.... It only does this while the engine is warm....when you first crank it and go it doesnt do it until about 2 miles down the road...when i changed the plug wires it stoped for about a week the first time,then returned then i changed the plug wires again which worked about a week then returned so i changed again but this time had no affect...new plugs and fuel filter also...I consider myself kinda mechanically skilled but this problem has me running in circles.. basically hopin someone had the same experience and could help me out thanx for everyones time....