I have 1996. Manual. 130,000 miles.

In neutral, let off the clutch a very slight whirring noise. I say very slight. Clutch in, it's gone. My research has said input shaft bearing. This may or may not be related, but my transmission 'slips' if I accelerate any harder than normal above second gear. I say 'slip' because I continue to accelerate, but very slowly and the rpms increase rapidly.

My research seems like this means new clutch, but from what I've read this is usually accompanied by having to push the clutch in farther than normal to shift. This is not my case, I barely have to push the clutch in at all.

What say you gentlemen?

 

Yes clutch is worn out. When it releases when you barely touch the pedal and slips under heavy torque, it is worn out. While the transmission is out of the car, take it apart and replace the input shaft bearing(s). Usually it is the one on the outside end of the shaft.