before i begin, forgive me for i am not mechanically inclined

long story short, reduced power and service traction control lights paired with a tac module code (P1516) on my 07 GP prompted me to replace the throttle body unit with one from NAPA. code went away and my car stopped giving me a reach around on the highway, but now the accelerator just feels weaker somehow. used to take very little to get some rpms and now it feels like i have to press halfway down on the accelerator pedal before my car actually does something cool. either im delusional, i need to perform a throttle body relearn (i do have a custom tune, this could make sense), or there is some other pressing matter of which i am too inept to see. if it makes any diagnostic difference my vehicle is not stock, but rather has been cursed with a: downsized pulley, zzp cai, hi flo catted downpipe, tune, colder plugs, colder thermostat (everything in the stage 2 zpp kit). please help and thanks in advance