You can rule one thing out then, the noise wouldn't be the pilot bearing. When the clutch is engaged as you're driving, the input shaft of the trans and the engine crank/pilot is all turning together at the same rate. If it was the pilot bearing, it would make noise when the clutch is disengaged or when the trans is in neutral.
Does it sound like a gear whine?

 

its hard to explain the noise. i wouldnt say it was a gear whine. More like a bad bearing kind of noise.

thanks for all the help.

 

speedo cable maybe?

 

i took it back to the guy who rebuilt the transmission, and hes going to give me a call tomorrow with the problem. Ill keep you guys posted and thanks for the input and ideas

 

im saying its a bearing on the output shaft, possibly the forward bearing. with its location, it is directly behind the input shaft so it sounds like its around the bell housing. the shape of the bell housing can amplify the sound because, well, its shaped like a bell.

my brother's s10 had a bad pocket bearing and mind a grinding/crunching noise through the shifter and was amplified by the beer tap shifter. it was engine speed dependant and would go away in 4th gear with the input and output shaft speeds were the same

 

so, the fifth gear bearing had came apart and a piece of the bearing got stuck making that noise.

 

Hate when that happens! Were the bearings replaced with the rebuild?