Vortech 07 GT Mustang Auto 3rd to 4th gear stacks real quick.

Hi My vehicle is a 2007 Mustang GT with Vortech supercharger standard kit, Auto Trans, only mods are 3.73 Gears and supercharger, ever since I installed the super charger my car has been shifting kind of strange, not very smooth, but also 1st to 2nd shift at Wot is normal, but then 3rd to 4th is extremely quick, almost stacked right on top of one another, so at the track the car Kind of bogs between these areas because the shift is to soon, Now I have tuned f-bodys before and I know that with a 1998 Z28 Camaro Auto, with a real low ASA Cam like 110, the map sensor cancels out the MAF or vice versa, and so the trans stacks the shifts as well do to the lack of vacuum, because the ecm can't decide what the engine load is, and this transmission behaves the exact same way, because engine load is Determined by the map, and the trans just doesn't shift right, well same issue kind of with this 07 Mustang GT. So my question is with a Forced induction Mustang with automatic Transmission is there any special parameters that should be disabled or, any numbers that need to be increased or any settings that should be altered given the setup, I have Hptuners, and the canned tune that came with the diablo programmer, I can't edit the diablo program after its installed on the ecm, and this verison doesn't have any shift settings that can be edited, but I can edit before and then install the diablo tune over it and it will use the shift properties set before the diablo install. because when the diablo tune file was made by vortech they didnt modify any shift settings, Thanks