What are you looking to do with a manual? Are you planning to go faster? Or do you like the ability to shift and look cool? Any racer knows that it is easier to stay the most consistant with an auto, autos will shift faster (some even do it while the front is looking up at the sky), and in some cases you have less drive train loss than you do over a 5 spd. If you are doing it to get faster than your pos auto think again with the right stall your pos auto will be faster, if you are doing it to look cool how cool would it look if that stick guy got smoked by an auto. Yes comparing a stock 5 spd to a stock auto the 5 spd will win, but comparing a slightly modified auto to a slightly modified 5spd, I would put more to the auto than the 5spd.
My suggestion would be to hold off on the cobra, keep your "fobra" (ssotn Adam Drugger lingo) and put a little work into it you will be better off being that you won't have to do the performance upgrades all over again, but if you like loosing money and like doing things a second time around go for it, no skin off my back.