Im also been having this issue with my car. Had it for about a year, and just started hearing this noise about 3 months ago. I took it in about a week ago to my local ford dealer, was there for a total of four hours. I took the shop foreman for a drive, he did hear the whine and couldnt make out what it was. He then told me he was going to take the ( quote on quote "transmission specialist" for a drive. So i sat around for about an hour till that happened. I then was approached by the service rep that took in my car and she explained to me that, they believe it has something to do with my "mods" and that its coming from the turbo??. Then the shop foreman came to explain the same thing to me?? saying that both him and the "head transmission specialist" believe my turbo is making the noise. By then i was fustrated and wanted to speak to a real mechanic which apparently there wasnt any available. I explained that there is absolutely no way that my turbo is somewhat damage as i still boost the right psi. It clearly sounds from the drive train, specifically the output shaft bearing as i had read on here before. They refused to believe me, so then i spoked to the service manager, we went for a drive. Little to say he was intrigued by the noise and said hell look into it. Week went by he had no answers, i guess dealerships that have replaced bad transmissions on the ST's havent reported it to theyre "hotline" or something like that so there wasnt any history of the issue. So now im scheduled to bring in my car this tuesday coming up for them to fix a perfectly good turbo, and if that doesnt work thats when theyll look into the transmission??. I just hate to have my car there even longer just based on the fact that these "transmission specialist" are so damn naive.