Car problem after warmed up ..Hestitates

Heres whats happening. I never noticed this before cause I never took my car on long long highway drives.

Now as a quick note, everything seems to work fine when the cars cold.

After about 1 hour driving at about 75MPH on the highway, and decide to pass someone, and downshift to 4th to get a quick leap, my car hesitates after passing the 3000RPM mark. as if I just hooked on a trailer feel.

Now at about 2 hours driving. and I try to attempt the same thing. The car hesitates as if i was trying to take off from 4th. The car shakes even worse almost causing whiplash in 3rd. (pretend your in forth and you pump the gas pedal like your bleeding the brakes) Thats how it feels.

OK so at first we thought it was clutch because I had slippage. After $400 later on a clutch the same thing.
If I press in the clutch and rev the engine, It redlines with no effort. Another words it goes between 3 - 4000 RPMS great.

Nobody knows. Also if I shut the car off for about 30 minutes and take off, its fine again for about 20 minutes then back again to the fluddering problem.

A few things I though of was a gas pump issue, but why after its warm and runs fine in neutril?

Any guess people.

My cars a 99. I changed the Fuel Filter and cleaned the MAF, I haven't taken it on a long trip sense. My car only starts to lag after 1hr driving and runs top notch before hand. No I have no issues starting up cold, although we have hit winter yet. Thanks for your input.