Every time i am in second gear at about 2000 rpm in my 99 SE, a deep wining sound is heard. it seems like its coming from the rear. Maybe its a bearing? i don't think its the clutch because its fully engaged. Has anyone had this problem? All help is appreciated.

 

I had a deep whining sound once on a manual transmision at any speed and rpm, on reverse. It was coming from a gear with a broken tooth.

I am not suggesting this is the same problem you have, but just speculating. If the sound is heard only when transmission is in a same and specific gear though, I would bet on that.