a couple of things...
1. it's fine to have the DTC's set to either 0 - MIL on 1st or 2- No MIL
2. log the Dynamic Cylinder Airmass (g/cyl) in the scanner (the Dynamic Airflow values are calculated from the dynamic airmass but are limited to 512 g/sec, but the dynamic airmass is not limited and is what is used by the PCM for fuelling and spark. You shouldn't have to set the Boost VE to anything close to 4096. Also log the GM VE value.
3. get a fuel pressure gauge on that engine and check the fuel pressure to eliminate a pump or other issue.
4. make sure your MAP sensor is calibrated correctly by comparing against a known good boost gauge or something. Also check your baro reading in the scanner to ensure it is somewhere around 100kPa. The scanner is showing a lot less than 12psi boost.
5. Check your wideband