I recently had my gears swapped to 4.10 from 3.90, I started to get a funny whine in them around the end of last summer ( the 3.90's). I figured it was the gears, and I would just go up a notch and that would replace the problem. I took it to a guy I trust, a local guy who has done lots of work on my mustang, and my friend's bullit, and did alot of work on my cougar too.
However, I still have the problem. I hear it after I start to slow down, under 30mph, usually coming off of going over 50. I also hear it when i accelerate up to 30, but again, it's usually after i have slowed down and started to speed back up. I cannot tell if the noise is there over 30, because my exhaust ( thanks mustangtuning!) drowns it out if it is happening.
The mechanic heard the noise to and didn't think it was the gears, so he checked all the wheel bearings, they all looked ok, and greased them and some other parts up.
It still is happening!! To me, it sounds like the drivers side rear, a whine, or soft whistle, like a long bird chirp or something. My girlfriend seems to think she can hear it from the passenger front side. I can only hear it from in the cabin under 30, or with the windows down under 30.
Any clue as to what I should ask them to check out, or look at? I let him take the car home for the weekend, I trust the guy with it ( you should see his old school fastback).
The noise is really getting on my nerves.

 

have you looked to see if the exhaust was rubbing? I know i had a chrip on mine and it was comming from the passenger rear side. I had them put it on the lift and it was the exhaust rubbing. i'd try that out. I could be wrong though

 

i have a gear whine and its only when i decel from 50-40. maybe your rear brakes are making the noise.

 

LIke everyone else already said...check youe ex and brks to make sure it's not from that also your u-joints, they generaly don't whine or will also cause a chunk or cluck sound/action as well. some gers wine no matter what usally higher #s. I have 4.10s(motives) in my 99 and they whine a little 30-50 but my 04 with frpp don't make a sound(same gears 4.10-set up by the same guy). go figure??

 

Is it loud or just a low hum. Lots of after market gear shum. Mine always have too. But, I recently used Royal Purple and the hum seems to have vannished. Go figure.

Good luck and hope you find the problem.

 

Lots of people (myself included) have whistles or chirps after we installed a TB or plenum and it seemed to be under the same deceleration conditions. Not sure how certain you are of it coming from the rear or not.

 

How many miles do you have on the car? When you swapped gears did you replace the bearings?

could it be coming from the driveshaft?

 

bout 70k miles, only needed one bearing replaced, they were all less than a year old (when the 3.90's were put in). its not a hum, more of a whislte, little high pitch, but not overtly loud.