I recently bought a set of headman shorties 1 5/8" with a 3" collector to replace the 1.5" with 2.5 collector no name headers I had. I also replaced the 2" y-pipe to a 3" single pipe that led to the muffler (flowmaster) to dual outlets. I replaced it with a 3" crossover from the drivers side header to the passenger side header which routes a straight 3" pipe to the muffler (magnaflow) with dual outlets. a rather larger type muffler that the one I had.
now the engine runs like crap. almost as if one cylinder where shut down but after testing compression on all cylinders and cleaning the plugs still runs like crap. could it be the crossover?

 

Got a pic of this setup? I'm having a hard time picturing it.