Your headers will not fit the DOHC heads. Your mid-pipe, I believe, will not fit either; however, if you have longtubes on your GT than your shorty-midpipe will probably fit if you get longtubes for the DOHC Cobra engine. If you keep the SRA, your GT cat-back will fit. If you do an IRS, you will need a Cobra cat-back.
You do not have to have the IRS, unless you are tring to build an EXACT clone of an 03 cobra. Something to consider, is that a lot of the 03 Cobra buyers did an SRA swap for better durability especially in drag racing applications. With an IRS you will have a bit better ride quality on the street, but nothing so significant to warrant an IRS swap.
Matthew 26:52-54 / Go Pack Go!
1987 Mustang GT Hatchback - 2V Mod Swap In The Works
1997 Lincoln Town Car, PI Intake/Cams, Sofa-On-Wheels, "Fat Tony" we call it
2001 GT Convertible - D1SC / Geared / Cammed / 440wh 400wt - TOTALED 2/2019