This is currently set to run in pure filtered MAF. Dynamic airflow is being entirely derived from that. What's the background on this tune and the components changed? Read off the injector part number first of all. Anything else you see that sticks out, too.
Only after that's taken care of, and settings in the tune are correct, then move on to VE.
The disabling the MAF part: Load the attached. Use Scanner>Vehicle Controls and Special Functions to clear LTFT's. Run it and post a log. The tune is set for SD. Few changes. I reduced the Low main spark table to stock for safety. RPM limits reduced in case a shift is missed, not to mention Gen III rods. Deadband added to LTFT enable.
What a hack of a tune btw. A very basic example is the file is called 6.0, but the tune shows 5.3. Shift RPM's are above the safe limit for the 4L60E. Spark exceeds MBT. All kinds of stuff. Want to get it straightened out after? Let me know.
Or if you don't want me messing with it then kick it up to the pro's:
https://forum.hptuners.com/member.php?4408-edcmat-l1
https://forum.hptuners.com/member.php?33521-GHuggins
https://forum.hptuners.com/member.php?5378-Alvin
Either way the tune needs gone through entirely. It'll solve a lot of problems, even the ones you don't know are there.