what are you trying to accomplish here? do you just want a cobra motor to say you have a cobra motor? seems pointless to me. the cobra motors are 5.0L 302cubic inch just like your gt motor but with some different heads, cam, rockers, intake, injectors, and computer. Now this is just stock ford parts. there is a plethora of aftermarket parts that will perform much better than a cobra motor. if you want stock driveability just keep the gt and don't waste your money on the cobra stuff. if you want power skip the cobra stuff and go with twisted wedge or edelbrock or afr heads and likewise intake.
what's wrong with your engine now that it needs to be replaced?
a 302 has a 4.000 bore (the hole cylinder size) with a 3.00 stroke. the stroke is the movement of the piston in the cylinder. a 306 is the same stroke but bore out .030(commonly referred to as 30 over), which arrives you at the 306CI. this requires machine work of the block and different pistons. a 331CI increases the bore from stock to 4.030 and the stroke to 3.25. a 347CI increase the bore to 4.030 and the stroke to 3.40.
not trying to be cruel here, but you really need to look at the basics of the block before you start throwing terms around, your just going to end up confusing yourself. There is a plethora of information out there that is just waiting to be consumed. Also, sit down and figure out what you want from the car, whether it be performance, looks, stock, then we can help you decide. Also, this is stuff can get expensive fast so figure out a budget and what your willing to spend.
