Final update - the car has been done and was released back to its owners yesterday.
Upon arrival we scanned and found fault codes P0299, P0171, P015B, P0420, P2270 and P1101. The turbo had a crack (see pics below) and I found unmetered air entering from the pcv diaphragm on the valve cover.
Between diagnosing the issues, replacing the turbocharger (along with the oil lines and various gaskets), installing the new valve cover kit (included new bolts and gasket) and checking for an updated ECM calibration (car already had the latest one installed, but I went ahead and updated the BCM, EBCM and instrument cluster since they are already paying for the labor time and software charge from GM), the labor time was 6.3 hours. That breaks down to 1 hr for the diagnosis, 3.2 hr for the turbo, 1.1 hr for the valve cover and 1 hr for the software updates. The total list/msrp price for all of the parts (including the GM SPS access fee), including tax, was $1010.96. Labor rates vary by geographic area, but independent shops average $120/hr here and dealers are in the $160/hr range.
The customer approved replacing the spark plugs, oil and filter (found hard carbon deposits and some sludge in the oil return tube), air filter and cabin air filter for preventative maintenance, but declined resealing the engine oil pan, brake fluid flush, drive belt, the suggested cooling system updates (expansion tank, hose and water outlet), wiper blades, rear tires and the screaming engine water pump (there is a warranty extension to 150k).
Turbo:
The obligatory valvetrain picture:
New valve cover and turbo installed:
Checking for ECM software calibration updates using GM SPS and a CarDaq Plus 2: