Luis.A,
The stock intake can be ported to flow WAY better. Your main concentration should be in port matching the TB, the upper to the lower, and the intake to the heads, and runner #5. Runner five has a huge dog leg in it do to a intake manifold temperature sensor. IMHO, that sensor is worthless. So I ground right through the boss, and filled the hole with 2 part aluminum epoxy. I then rewired the sensor and left it in the wheel well. Never threw a code, so I left it that way. You can also remove a ton of stuff from the throat of the upper. It bottle necks where the center bolts that connect the upper and lower are located. You'll need a long shafted cutter, like the set of three Summit sells, to reach that area.
There are conflicting stories on the GT40P heads. Some say you need to dimple the header, some say you don't. In a Mustang, I'd only go with the GT40P specific headers. On the Cobra, the stock or stock aftermarket may work with a good set of high temp wires.
As for HP, that's a total guess. I'd say you'll be happy with it for about 9 months. Then you'll read about 90HP gains from a used Vortec you can buy for $1,600. and bolt on in a weekend. Then you'll want more, so forget how much HP it has, and concentrate on how it feels! Will it be fast? Does an elephant have big ears?