I just bought this car and when I'm driving over 35mph I hear a whining kind of sound coming from either the tranny or rearend. It is a 5 speed. When I'm on the highway way going 50mph+ the noise is louder and faster. When I put it in neutral or put my foot on the clutch it stops completely but starts up again as soon as I put it back in gear and give it gas. It does this at low speeds to but the noise comes and goes. Please help and thank you in advance.

 

The fact that it stops when in neutral, makes me think that your rear end is good. It would still be making the sound in neutral as it is still turning while going down the road.

If you haven't already, I would change the oil in both the rear end and the trans inspecting the old for any signs of damage being done. I would also try to have the clutch and flywheel inspected.

How many miles are on the car and these respective parts?

 

It has 180,000 on it now so I assume both the tranny and rearend also have 180k. I just checked the trans level and I can't tell if there is enough in there or not. I pulled the fill plug but nothing came out so I'm hoping it's just low and just curious, do these cars use ATF even though is a manual trans? The trans fluid was also a little dark and not red so I'm really hoping that's the problem.

 

Not sure about the gt's trans, but my 2000 v6s T5 used automatic trans fluid. Mercon V I believe. It should be in the owners manual.

Not sure what all you've done since you bought it, but I would defiantly change all the fluids, spark plugs, maybe wires, fuel filter, and clean the MAS.

 

99 Mustang GT came with a T-45 transmission. Factory specs are 3.1 liters (6.6 pints) Mercon ATF. Not Mercon V.

That said I think a lot of people experimented with GM syncromesh fluid.

I have been running 10w30 synthetic blend motor oil and a tube of K&W friction modifier in mine for 60-70,000 miles with no problem. That and a UPR shifter made a world of difference in the way it shifts. (try at your own risk)