have a scanner put on it and see if a sensor is out of whack.or pull the injectors and have them tested

Any chance you are having fuel bleed into the manifold and flooding the motor? Typically advancing the throttle on an EFI motor will enter the 'flood clear mode' which will shut down the injectors allowing air to clear out the excess fuel. Sounds like this is your problem. I'm not really familiar with the later cool fuel systems but do know that previous VST systems had several issues which would cause flooding when certain inner diaphragms of the VST would deteriorate.

he has a gen 2 cool fuel and clear flood mode still applies here. I would do a fuel pressure check and make sure FPR is good and its related set up.

Also check MAP readings - A bad MAP or out of readings can cause rich conditions