The MAF and TB will be a nice addition for the intake side...not sure what sizes you should go for though... I'd probably get the 70mm throttle body. Heads will make a big difference, but they are pretty expensive. The stock heads will allow for a decent amount of power...but a board member on here told me he saw pretty good numbers running the stock heads, but heavily ported and polished....that's up to you what you want to do. I don't know how good the GT40p heads are....what are the valve sizes on those? Ideally you want 1.9/1.6, or 1.94/1.6 valves. My Performer RPMs work very well but at $1100 american for a pair..they aren't cheap. I've got a Cobra intake and it works pretty good but I'm sure the Trick Flow one is better. Like you said, the Cobra is old. Headers....all I can say is I'm prejudiced against shorties...unequals are much easier to work with. The equals might make more power, not sure..but they EAT spark plug wires for breakfast..if you go equal-length, invest in some boot protectors! I'd go with longtube headers though..they really are the best....and they'll sound good with a new set of heads. Heads tend to make shortie headers sound like crap...my exhaust sounds horrible now solely because of my equal-length shorty headers.
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