2000 Honda Civic Car Grind Noise

Hey, so my car has this odd grinding sound that often comes but few times it does not. When I accelerate in 1st gear everything sounds fine til I hit about 2000 rpm and then I hear a sudden loud grind noise of metal contacting each other and it continues til I shift to 2nd gear, above 2000 rpm or so the noise comes back, once I hit third gear the noise goes almost away completely even on high rpms and same with the higher gears. I have jacked up the car and revved it past 2000 rpm on 1st and 2nd gear and noise is not there, its only ever there when I am driving. The fluid for the Transmission was checked and was leveled and clean, Engine fluid was fine too. Everything shifts fine and dont ever have any problems other then that noise (Which gets pretty loud) one thing to mentioned is I do think the Input shaft bearing is bad since it makes that common slight grinding noise in neutral when you start the car. Everything is almost stock from what I was told. We do also have some worn engine mounts but would that cause such a noise at specific RPMs on low gears? Also when the car decelerates in those gears with engine braking you get the same nasty grind but once you hit the gas it goes away. When we hit the clutch pedal, noise also goes away.