lly maf adjustment for s366 with 4 inch intake.

The truck is an 04.5 lly, built trans, dual cp3, 80% over injectors with a billet s366 fixed vane, built engine rods, pistons, keyed crank and cam, studded. I have tuned on this truck for a while, it runs really well except in the first 3 gears on wot it will make boost up to 40psi then cut back to 30psi until it hits overdrive/ lockup then will increase up to 48psi and pull hard. I know in 5th lockup it is loading the engine harder and making more boost. Question is in the 3 gears when boost ramps up to 40 then drops off is this an issue with maf as I have not adjusted it. I have looked this tune over several times and do not know what I am missing unless its just not loading the engine hard enough?