I have a VCT zetec, and it does not like to be modified

. I put a CTA intake and a crankcase ventilator on it once, and it didnt like that. The CEL came on, the RPMs would drop, and it would die. I have SVT front bumper and grill, and would like to get the SVT side skirts and rear bumper to match, but if im going to get that rear bumper, i have to get dual exhaust, it wouldnt be right without.
My question is if i put a Y pipe after my CAT, would that change my exhaust flow enough to bother my VCT? maybe 2 stock mufflers would work best?