I have a 99 mustang gt & I know it needs either a pilot bearing or throwout bearing, but it started making a knocking noise when the car reaches @ 2200 rpm & stops after I shift gears! Does not knock in neutral, only when gear needs to be changed

5.000rpm's high revs and you run into problems with valve bounce ( hitting pistons) ,ring slap, gudgeon pin knock, big end noise and possible main bearing noise . You may also be getting a hydraulic lock in the hydraulic followers that is holding the valves open too long. Unless the engine has been specifically built for these rpm's any loose ,worn on unsuitable part will cause problems I am thinking that you have around 100.000 miles on the clock after 7 years and the motor is not young Ford V8 engines specifically built for a 500 klm race are limited to 5.500 rpms because they destroy the timing chain if driven over that speed .

1. Brake booster diaphragm may be torn.
2. Tie rod ends may be failing.
3. Likely lifter noise. Change to better oil and oil filter.
4. Hood stops need adjusting.

You need a mechanic.

as the knock get louder with acceleration, it indicates a bearing or camshaft lobe problem
you will have to check the history of the engine or the rebuild of the engine

The throw out bearing slides on a collar behind the input shaft on the front of the transmission inside the bell housing.
It will require removal of the drive shaft, shifter handle, transmission, & clutch cable to gain access to it.
Recomend having this done by a professional.

throwout bearing or pilot bearing.did you replace those when you did the clutch

3 quarts should be enough fluid. Did it make the noise before you replaced the clutch. It sounds like a bearing in the trans. It's not the pilot bearing. A pilot bearing would make noise when you step on the clutch and then the noise would go away when you let out the clutch. Can you describe the noise? It sounds like a bearing in the trans or a problem with the throw out bearing.

The cutch pedal should have about an inch of free play before contacting the pressure plate. otherwise throw out bearing will run continuously . It wont last long. Adjust at firewall for 1 inch of free play at the top of pedal stroke.

Throwout bearing is going out so it means you would have to remove the transmission, and also could have a bad pilot bearing out and or a broken clutch spring so it would still need to remove the transmission to fix it and then If it where me I would do a clutch job on it.

throw out baring was inproperly installed

I use a really long 3/8 drive extension to reach the top bolts on the bell housing. It really is a pain to get to.