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P0610 has popped up on the forum from time to time and shows as an automatic transmission miscoded in the ECU, IIRC, as a manual transmission and I can certainly see that impacting turbo performance. If MRausch82's suggestion doesn't fix it I'd recommend contacting Keith at GDE IIRC he can fix this problem as part of a GDE tune which you need to get if you don't have one or advise you on a replacement ECU.
On the sound have you checked 1) both intercooler hoses for cracks/holes/etc and 2) the airbox to turbo hose for a split on the bottom just in front of the turbo (FYI be sure to push the upper end of this hose onto the airbox outlet until it touches the MAF sensor before tightening the clamp lest you crush the plastic airbox outlet)
_________________ Sold to LOST member my 05 Ltd, GDE Stg II turbo + TCM tune, SunCoast TC w. Transgo kit, Steiger window regulators, Samcos, Fumoto valve, 2nd gen filter head with Lub. Spec. bleeder, Hayden clutch & 11 blade fan, inverted spare, P-1 battery, BF Goodrich Long Trail TAs, Etecno1 glow plugs, timing belt at 50K miles/8 yrs
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