90 Mustang Rear End Noise

I just got done installing a motor into a roller i bought and it has a little rear end noise. its a 5 speed and I can only hear it in 3rd through 5th. Its a whirring noise i guess. i can only hear it when on the gas. i let off the gas and it stops. what do you guys think it is? i appreciate the help!
 
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Check the backlash on the gears.. It could also be the head bearing in the trans, check the fluid level or change the fluid if it has been awhile, you can usually feel/hear this through the shifter as well.

If your in 2nd gear and you push the clutch in does the noise go away?

Typically a rear end noise will show itself in all gears, but a trans noise can be selective in where it shows up at times
 
Thanks for the reply! but yeah it may be the transmission, because its only 3rd through 5th. and in those gears when i push in the clutch the noise does go away. So its the trans? It does have a slow leak from the speedometer cable hole.
 
Yeah Id first try swapping the fluid out and getting it back to the proper level.

The drain plug is on the lower passenger side of the trans, the fill plug is above it (takes a 3/8" ratchet or extension) ATF/Dextron III. Fill it up to it is just below the fill hole.
 
Could be the gears in the trans themselves. If they've got a few miles on them, they'll get loose and wear into a pattern. I just replaced all of the bearings in my T5 this past weekend, topped it off with nice lean ATF and I've still got gear whine.