spark knock?

Hey everyone hows it going I just finished a pi swap on a 98 gt.My mods are a chip,k&n filter,2chamber flows,3.73 gears.My question is we put a off raod h-pipe in the car 2 weeks after the swap and for some reason it runs worse.I'm not sure if it's spark sknock under load but the car sounds "airy" and makes a noise I can't really describe when you really get on it.This happened after we put the pipe on it ,I can't imagine why this would matter so much do I need to call the tuner and have some timing pulled.This makes no sense to me ,anyone with a suggestion please speak up.I guess the noise would sound like a "knock".thanks in advance.

thanks for the replys I was leaning toward exhaust leak ,I changed ecu and had to have the tuner turn off pats because it woul'nt start .I was thinking off swapping the old ecu in and seeing what happens.