my car has a hesitation at certain spots in the throttle and when it shifts through gears it seems like something is hold it back unless you put your foot down to the floor it runs like a champ, it shifts into overdrive at 35-40 mph.  2001 mustang gt 4.6 sohc auto trans cold air intake pypes x pipe no cats flowmaster exhaust.........  

I had that same car with a simliar problem.  First if you don't know about the Idle Air Control problem with it getting dirty, you should.  The big pipe CAI with oiled air filters are great, but they make your idle air control and MAF sensor dirty.  Clean them both.  Take the IAC off and clean with carb cleaner.  Let it dry and then put it back in.  Quick fix.  It sounded like you might be having a hesitation in the transmission.  I had this also and a simple transmission system flush and refill fixed.  Remember to change the filter also.  A good rule of thumb for serviceing transmissions are every 30,000 miles.

When my tranny was acting up, it almost felt like the car was surging at lower speeds, 35-40 when the car would shift into OD.  And a slight vibration at the other shifts.  But under WOT it had no problems.

try checking your egr valve and related componets that was the problem with my car it did the same thing i had to change the egr valve and take the controll unit off and clean it out it was cloged