your right, your cobra intake is fine, and you would be wasting your money if you bought a different one, i think that didnt realize that it was a cobra,
also, dont the cobra's have 65mm throttle bodies too? if so thats one more thing you dont have to buy, your mass air meter is also larger than a GT but still not too great, the same goes for your computer, i've heard that thing really kills the performance of the 93-95 cobra's, could be wrong though
about the "chargers" your probably thinking of turbochargers that would facilitate the use of a different header, plus they are hard to tune and very expensive so, being in college my self, i dont see that as a possibility for you, the same with the supercharger (not hard to tune, just expensive)
i'd go with the new 76mmC&L mass air meter with the inlet tube, very easy to install in little time and right about $200.
your motor as it sits has great potential to make great power, you just gotta get it out of it, your heads (GT40 irons) will flow awesome with a good port job, this with a combination of a good cam will make that thing scream, BUT if its your only car it will be kinda hard to pull the heads/port them/ and install a cam in only 2 days
hey just wait till next summer
good luck