Be more specific, which stock PCM/ECM? 02-05, 06-07, or 08-09? All are VERY different beasts to tune. You would have the best luck with a 02-05 PCMs or a 08-09 ECM I believe, the middle ones have lots of tables we cant see. This is my educated guess on the topic, honestly the only reason I can think of to not run VVT is if you have cam blanks that dont support it. Other than that, VVT is the reason the I6 makes as much torque from 1800+ as it does and the upper end HP.EFI,
Do you know of anyone running the stock ECU without the Exhaust VVT connected?