Thanks for all the replies guys but to clarify I would be buying a cobra that is already modded with around 20k miles and i'm looking to stay in the 24-25k range. So in reality I'd being buying a 2011 GT for 35k + 3-4k in mods to run near what the termi would run and equals to a 14k difference after mods. Now the warranty is a huge bonus for 2011. Also this would NOT be my daily driver I have a Navigator for that and my credit is a none issue.
My 03 had over 24K in mods on it.
For power it had long tubes, OR H-pipe, cat-back, tune, 2.76" pulley, ported plenum, big oval t-body, BIG MAF meter, Steeda CAI and various other small things and it had 450 rwhp. It would run low 12's all day and with a good driver it would see high 11's I would bet. The new GT can run 11's with slicks, x-pipe, cat-back and tune.
Shelby is already making a blown GT350 with over 500 hp (some are guessing 556) with the new 5.0
Now 25K MAY find you a lowish (around 30K miles) mile car and will prolly have exhaust, tune, intake and pulley to run 440 ish at the wheels. The STOCK GT will run with it with ease but stop MUCH better (with optional brakes) and handle MUCH better as well as be a more pleasant place to be inside.
Another thing to consider is financing companies usually give a much better rate on a new car then a used one so the payments may be pretty dang close.
Down side is in 5 years the GT will be worth 18-20K where as the Cobra will still be worth what you paid for it..... most likely.