I have a 2002 Mustang GT with a rebuild engine. Transmission had problem, replace it, still have problem.

Hey Scotty,

I have a 2002 Mustang GT that I put a rebuilt 140k mile engine in I also put in a new clutch when I did this. Last week the transmission started making clutch noise and was very jerky, the car would not want to go past 2.5k rpms and started jerking real bad, it didn't feel like a clutch slippage though.. I figured it was a TOB but the gear noise led me to go ahead and replace the transmission and replace the clutch set. I did all of that and put in a 80k mile TR3650 transmission but I still have the same exact problem. I am going to try and seat the clutch fork in further because the fork seems to be sticking out too far and the dust cover wont fit it even though the fork seemed fine and clicked into place. There is a good bit of vibration and the rpms will wiggle, this is only when the clutch is disengaged, when engaged the engine runs perfect. Would the differential cause anything like this? I was thinking about checked that out because I have not yet, could a clutch cable also do something like this? I am just very confused about it.