Just wanted to add my 2 cents. I had this exact same problem. 2011 GT with 67k miles that i was going to buy used. Test drove it and it had a noticeable whine in 1st, 2nd, and 3rd. It happened mostly when the gears were under load (especially slight load) and the higher the rpms the louder the whine. I refused to buy the car until it was checked out. It was sent to a reputable transmission shop by the dealer i was buying it from, and the guy told me that he has seen a lot of MT82s with this issue. he didnt get a chance to tell me exactly what caused it, but he rebuilt the transmission.. the invoice shows that he replaced 5th gear, the input shaft and bearings, and the front/rear seals on the case. Once i drove it after that the noise was gone. Ive put 2,000 miles on it since then and its perfect.
Im not sure exactly what the problem was, but im thinking it was in input shaft bearing considering the nature of the sound. Anyone ever had this problem resolved in the same way? I just want to get some info out there and see if anyone had the same fix done with satisfactory results.
2011 Mustang GT, Kona Blue, Saddle Interior
Mods: Pypes 3" Offroad H pipe, Flowmaster American Thunder Axleback, Deleted resonators, Bama 93R tune, JLT Cold air intake.