The 03/04 cobra motors are nice, but I would never buy one used, unless it's a smoking good deal. Most people ask between $2,500-$3,000 just for the short block. It's a good short block, but you are still paying that much money for something used and abused, plus it has cast pistons.
If your talking about doing a long block swap, you will end up with a ton of money, in yet a stock short block.
I would look at building your short block, some MHS heads and cams, and a Kenne Bell 2.6. It will be cheaper than the route your talking about, make just as much power, and the short block will be brand new and be good for more power.