You've purchased and installed some "high performance" parts for your vehicle and had the ECM re flashed so that you are getting the most out of your engine but something still isn't right. Your transmission is shifting well below your torque/power curve. When the shift comes, the engine bogs because it is out of it's peak torque/power range. Here's an example!

You've modified your engine so that it will rev to 6800 rpm. When you "mat" the go peddle your engine performs well but the transmission shifts 1-2 at 4400 to 4500 rpm. Since your engine is capable of revving another 2000 plus rpm you are more than likely just entering the peak torque/power band of your vehicle when it shifts. The shift drops your engine's rpm below the peak torque curve and causes bogging until the rpm's reach the edge of the torque curve again.

Since shift points now days are controlled by electronic solenoids rather than spring tension or vacuum, modifying your transmission shift points must be done electronically. Bringing your transmission shift points to the top end of your torque/power curve will increase your zero to top-end speed or anything in between because your engine stays in its power curve during crucial shift times.

NEXT - MODIFYING THE OUTPUT GEAR RATIOS OR 0 TO 60 IN < 3 SECONDS