I have been looking at a 2003 F350 6.0 with about 42000 miles. The turbo has a high pitched whine that gets progressively louder as you accelerate. I asked the dealer to try and solve the noise problem and they ended up replacing the whole turbo with a new one. It still has the same whine. I'm now being told that the truck has an aftermarket exhaust that is larger in diameter than the original equipment and that is the reason the the turbo whines. Does that make any sense? How can the exhaust have an efeect on the turbo noise. The truck is perfect in every other way and has an almost non existent Oasis report, so it hasn't had any problems to date. I don't know if I can live with the noise that it makes at this time.
Any help that you can give me would be greatly appreciated.

Only a generic point of information...
There are Three souces of turbo whine.
1. Noise that is transmitted by the housing. Make sure the mounts are tight and any isolators are in place.
2. Noise from the intake. Make sure the filter is correct and sealed in place. Air and dirt leaking past the filter will quickly destroy the turbo and your engine. Next look for cracks and loose fits of the entire air intake. This can let dirt past the filter too.
3. noise from the exhaust. you have already said the exhaust is aftermarket. Check to insure the wastegate is closing. And check for exhaust gas leaks.

Over the years, truck manufactures have made the diesel engine quieter which makes the turbo easier to hear. A larger exhaust can decrease back pressure and increase turbo lag and be loader letting more engine noise and turbo whine be heard out the back.

Thanks for your help. I did some research of my own yesterday. I went to another dealer, who had a good selection of F250's and F350's on his lot. As luck would have it there was another 2003 F250 with an aftermarket exhaust there. I drove it and was amazed to hear the exact same whine coming from the turbo. I then drove an F250 with the original equipment exhaust and there was no whine. After looking into replacing the aftermarket exhaust with OE and spending upwards of an additional $1000 on the truck, I have decided that the truck that I was considering is not the truck for me. I just can't live with the whine being heard over the stereo. A little thing I'm sure, but the noise would have driven me crazy.