Rotating shouldnt make a difference unless, the rotor system was out of balance and had already worn a groove into the comp cover. Did you notice any damage to the inside of the comp cover when you had it off to rotate? Another possibility could be that the comp cover is not sat on 100% true (not sure how it is fixed to the bearing housing on a TD04 is it 3 tabs and bolts? or is it circlip? so has changed the front wheel clearance so when there is shaft motion (which there will be) it will touch. Have you spun the compressor wheel by hand firstly with the cover off, and with it on? do you find a tight spot? If turbo is shot the noise usually gets worse at higher speeds as the shaft flexes and oscillates more.