Lack of power sounds like vacuum wont shift

[Yamaha32088]

I just bout an 03 F350 with the 6.0 in it the only aftermarket stuff I have done to it is air cleaner and turbo back exhaust. After having the exhaust put on I noticed a huge downgrade in performance. I am not a diesel mechanic but after having the exhaust put on my turbo started surging really bad the wastegate would go crazy when taking off from a stop light normal not trying to go fast or anything. The problem got worse on the highways it sounded like an extreme highpitched whistle was coming from under the hood at the turbo and my truck at an idle started to sound like a vacuum cleaner not like the jet that is common with the straight piped 6.0's. I searched google for some of the symptoms and people said the egr valve could be dirty and to take it out and clean it so I did that and the wastegate quit acting up. I then took off the aftermarket aircleaner and put the stock back on and that took care of the super highpitch whistle I heard coming from under the hood at the turbo. The truck still sounds like a vacuum at an idle and still has a high pitched whistle all the way up to 3600 RPM which is usually when the truck decides to shift. There is no rumble in the exhaust just high pitched whistle all the time. On the highway the truck will sometimes drop RPM's and lose power and wont allow me to go over 50 or 60 unless im going downhill. Does anybody have any ideas what could cause thie. I took it to ford and they told me the turbo and everything else is working fine the turbo is building boost up to 28 PSI.