I am aquiring a 1999 Cobra from my father soon and am looking to upgrade. I was planning on putting a catback exhaust from Magnaflow and a short throw shifter. What else should I get in what order for the best gains? The car is completely stock and I intend on keeping the IRS for some corner carving fun.
Billetflow rearend brace, 4.30's, and some DR's would be a good start. Gears really help the N/A 4 valves. Aside from the wheelhop you will like the IRS as long as it doesn't brake. I install some Maximum Motorsports full length subframe connectors(which is another good mod for you to consider) and have almost gotten rid of all my wheelhop.
Is there anything else I should look into? I was thinking of putting some JBA headers a twin 65mm TB plus a K&N FIPK. I'm looking at possibly getting pulleys as well
If you can afford JBA headers, you should just go ahead and get a Sean Highland Racing 4V longblock.
That sounds like a good start, just be sure and get a tune for it. Matter of fact, go ahead and find you a good programmer like the XCAL and you can kill several birds with one stone.