Rear End Noise, Help Please

I have a 2000 GT convertible 5 spd. I have had the car since November. Ever since i bought i have had rear end noise, sounds like a hum/howl. I already had the differential rebuilt and had 3:73 gears installed, that helped the noise but it is still there just not as loud. The auto shop that did the differential told me that the remaining noise is because the rear passenger axle shaft was pitted, so i had them change that out. But i still have the same noise, now they are saying that they noticed that the other shaft is also pitted. But i don't think that a pitted axle shaft would cause this noise, due to the fact that it didn't get any better when i changed the passenger side shaft. Any help would be really appreciated.
 
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+ 2 on bearings. Also did you use Motive or Richmond gears?.. I have used both and used different installers whine/howl was still there. Only use Ford Racing Products! and i agree with the other poster to use a different installer as they seem to be strictly $ motivated! Best of luck :)
 
Thanks for the replies, sorry for the delay i hadn't been checking my post. I bought the axle shaft from Autozone and it came with the axle bearing so they should have changed it as well. I do notice the noise mainly when i'm going above 40 MPH, 4th and 5th gear. When they rebuilt the differential i gave them the Motive rebuild kit and i used Ford Racing 3:73 gears. I took it to another shop and they test drove it and said it sounds like something with the differential and suggested maybe they didn't use the proper gear oil or didn't put any anti-friction in. I am trying to avoid having to pay a different shop $200 to take the differential apart to look at it and then it not be the problem.
 
So i took my car to another shop and had them test drive it and told them that the rear end is making some noise. I didn't initially tell them that i had any work done to the rear end, just to see what they said without knowing anything. They confirmed that the differential is making the noise. I told them that i had the differential rebuilt and 3:73 gears installed and he said that they probably misaligned them when they were installing. Can you just remove the diff cover and adjust the ring and pinion or do you have to disassemble the rear end to make the adjustments? I'm taking the car back to the first shop to see if they will make the adjustments at no cost to me, if not i will be taking it somewhere else. Thanks to everybody for the replies and input, its been a big help.
 
What did they mean by "probably misaligned them when they were installing"? If the gears are whining from misplaced shimming/etc then you will need to take it all apart and put it in spec. If they replaced the clutch pak and failed to shim it properly or left junk or something (debris) I'd be really concerned with the quality of work already done and still recommend dis-assembly to redo said work.
 
The other shop i took it to the guy just drove it he didn't put it on a lift or anything. he said he heard the whining from the rear end and said the rear end felt "loose", i'm not real experienced with rear ends so i'm not sure. He was just throwing ideas out there since i did recently have the diff rebuilt and gears put in. The rebuild kit i bought was made by Motive Gears and then it was Ford Racing 3:73's, both were bought from American Muscle and were suppose to be good quality so i doubt it has anything to do with the parts use.
 
He must have an amazing butt dyno/calibrator to tell if a rear is out by a few thousand from spec. :)

My recommendation is to take the car to a shop with a good reputation for working on Mustangs. The rear will need to be opened up to check to see what all is in spec and if any bearings are in need of replacement.
 
So far i haven't been able to find a shop that works on mainly mustangs around where i live. I'm taking it back to the place that rebuilt the diff and installed the gears, they are going to open it back up and see if anything needs adjusted. When i had them rebuild the diff i bought a rebuild kit that had all the bearings that were needed to do the rebuild, so none of the bearings or gears should need replaced already. So we will see what happens on Friday or Saturday.
 
Took my car back to the shop, they opened the diff and reseated the ring and pinion. They also said that the wheel bearing that was recently installed with the passenger rear axle had broken apart so they replaced that too. And they replaced all the seals. Noise is almost completely gone except when i'm coasting. Another guy told me once that if the ring and pinion aren't installed correctly and you drive the car, there is not any way to get rid of the noise unless the ring and pinion is replaced. Is there any truth to that?
 
According to them they removed the ring and pinion and reset the backlash, installed 2 new axle bearings and seals. So since they probably did it wrong the first time and i drove the car like that the noise will probably be there until the ring and pinion is replaced again, which sucks.