I don't know if this is relevant,mine has been doing something similar.Funny thing is it has been doing this ever since I bought it in March of 2000.Head gaskets were replaced in May of 2000.I have a 5 spd manual trans.Only when it hasn't been running for at least a day does it do this.I'll start it up,runs fine,no shuddering,no misfires ..nada.I'll back out of my driveway within 30 seconds of starting it.It hesitates a little when i'm applying the gas and letting off the clutch,but it goes.Then I'll put it in 1st and start taking off.During the time I am letting off the clutch and gassing it,this it when it will start hesitating...during the immediate take off.As it's hesitating,if I try to give it more gas it will sometimes stumble and backfire a little.After a few seconds it will clear up.I will notice it in 2nd gear at the low end,as i'm letting off the clutch and giving it gas.It doesn't stumble like it did at first but the power can seem rather anemic then all of a sudden it clears up.After a minute or so,this problem is gone.Again,only when the car has sat for at least a day,after first starting it.It's much worse on very damp and humid days.More noticeable in early morning when the morning dew is still out.Don't know what causes it.I have done LOADS and loads of work + maintenance to this car for the past 9 years i've owned it.Everything from MAF sensor to all 4 O2 sensors,Evap control valve,wires and plugs a few times,coil pack twice, ran a fuel induction twice + all the other dozens of things I have not mentioned that has no relevance to this.
I brought that up as I thought theres a chance it may be related to what you're experiencing.Is it anything like what I described above? Is your stang an Auto or 5 spd ? Has any other work been done to it? Did it run like this before the work was done? Do you get a Check Engine light? I wanted to point to the MAF sensor but if this didn't happen before the head work then I highly doubt the MAF sensor is faulty.Unless some dirt or oil got in the sensor wire.You may want to check and make sure every sensor is plugged in.Check the Throttle position sensor to make sure that has no been unplugged (it's on the back side of the throttle body).
Has the car been sitting for awhile? eg..a couple months? Has the injectors been cleaned in the past year or two?
A lot of questions,yeah....A lot of things can cause the engine to hesitate so you need to rule these things out.