ok so my tranny is making a whining noise in 4th and 5th on the higway. also when im in neutral and clutch is engaged or disengaged tehre is a sortof a whine that slows to a pulsating whine when i slow down. my clutch was slipping bad so i replaced it whith a slightly used jdm clutch and flywheel. they were from 2 diff cars. now im getting a really bad grinding noise when ehgaging the clutch and the other noises have not gone away. i have a cpl ideas on it

1 the new grinding noise is the throw out bearing.
2 the new noise is the clutch getting used to the flywheel and getting broken in
3 i have no idea what the other noises are

any one have any suggestions before i go and buy a new gearset?