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93 cobra is a no, unless you have $10k.
94 & 95 cobra had the pushrod 5.0l v8, and about 240 HP. They respond well to mods, but I've kinda grown to think that body's kinda ugly (I had a 97 GT, same body), and the 5.0l as older technology.
96-98 cobra's are a DOHC 4.6l with like 300 HP, aka 4v (4 valves per cylinder). Again, early SN-95 body, but different ground effects make a big difference. These aren't cheap.
99-01 cobra is the same DOHC 4.6l, but with 320 hp, look fuckin sweet, and have something no other cobra EVER had, amber blinkers. Don't even bother with the 00 Cobra R, you can't afford it.
03-04 cobra, you can't afford, but fuckin own.
That being said, I'd go with the SN95 body with the SOHC 4.6l (aka 2v) (either is up to you, 96-98 and 99-04). If you get the early SN95 with the non-PI 4.6l, you have room to grow pretty easily. Unfortunately, the 96 & 97 only have 215 hp, and 98 had 225. However, you throw a set of PI (99-04) heads w/cams & intake and it'll bump you to like 265-270-ish (higher than PI motors).
On the non-PI motors, they had flat-top pistons with a higher cc combustion chamber. When Ford redesigned and came up with the Performance Improved 4.6l, they moved the fire down into the cylinders with dish pistons and lower cc combustion chambers. You combine the lower cc heads and flat-top pistons will bump your compression to close to 10.5:1. The PI cams are a better profile, and the PI intake has more volume. They're all a direct bolt-on, but have to go together, as the intake ports are different shapes between PI & non-PI. You could also swap in the 4v heads, but there's a bit more to it than just 'swapping'.
Then, all 2v 4.6l, for an additional $200~300, or so, you can get an aftermarket plenum (upper intake) and 70 or 75 mm throttle body, which is good for roughly 5~10 HP. You can pull one from a 99 model, as it's like 66.5 **CORRECTION = 66.8mm**(I think the biggest of all years).
Off-road x-pipe, h-pipe, or pro-chamber, non-factory mufflers (or throw in cat-back if you want), and you've got a nice exhaust setup. Most mid-pipe's run $100+, same with a set of mufflers, and never purchased a cat-back system.
The 4.6l responds to mods well, but the 4v doesn't have as much of a following as the 2v, in reference to aftermarket. ~Luke
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1969 Cougar - 11.91 - 380HP
2007 GSXR 750
1999 OZ - SOLD - 15.26 NA - 14.71 on 75 shot
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Don't sell your car to 16 year olds... 
