I have 2 transmission problems, maybe theyre related? The car sometimes pops out of second gear when accelerating, and at Idle with the car in nuetral, there is a rattle almost like a throwout bearing noise that goes away once the clutch pedal is depressed. I heard , maybe input shaft bearing ? Help!

First problem is probably synchros, although they are generally more notciable when decellerating.

 

The second problem sounds very much like a classic noisy throwout bearing.

I thought throwout bearing too ,except the noise goes away when the throwout bearing is engaged and turning, just the opposite of what you'd think.

It very well could be the input shaft bearing.