so, since you went back to the stock WGA, did you go back to the OEM-like tune to compare drivability/performance? Over here, the Cobb AP has a default tune that is similar to stock. As you are decatted, with prob throw error codes, but might be enough to quickly rule out issues with the WGA and boost control solenoid? Since you are using a different engine mgmt system, some speculation there on my part.
The hose routing on the boost solenoid is correct? Were any of those inadvertently changed when replacing the WGA? that can also cause very odd boost behaviors. Just something to validate if you havent already.
It is throwing off any fault codes that could help point you in a direction? I expect they would be different than our, but still something to check.
Is there another tuner over there that you can engage to diagnose?