MrBuffet You will have alot better and cheaper chance of finding a 390 with alot of meat in the cylinder walls than a 427 or 428. What ever motor you deceide on, Tell them you want a machinist to do a crack and sonic check before final payment. Sleeves in motors is another thing to have checked out.
How original is the car going to be? Iron block is find. You can save about 100 lbs with Aluminum heads and intake manifold. You will add about 50 pounds with an A/C system. What trans are you looking at?? 4 spd,5 spd, 6 spd, or Automatic??
If you are going to have a motor built, the top 3 are already names above. Building an FE motor is NOTHING like building a BBC or SBC. There are not alot of machinist out there that know what they are doing and how needs to be upgraded to get many years of life out of an FE motor.
If you want an FE motor under the hood, a 390 stroker out to 445 will make you a happy owner. A ton of torque to move the car with A/C running and still quick and streetable for years of fun driving. Cost should be about 6-7,500 dollars built with machine work and a stage 2 set of heads from KCR or Barry R's shop. Shop hard, watch out for used parts.
The manifold needs to go to Joe Craine for a cleanup and balance of the intake ports in the manifold. He will equal the flow to all cylinders. On some manifolds there is a 20-45 cfm differents in flow. Big thing is a name plan and stay with it once you have what you are looking for. You will need a 130 amp charging system. Most cobras come with 60-70 amps and external voltage regulators.
A stroker windsor motor will work as well and cost a little less. There are some nice 408-427 stroker motor on the market that come with 2 year warrantitys. A good selling point if you are going to abuse the car hard. If you can talk to one of the Smith brothers, they also might shed some light on your ideas and buildup of your cobra. Good Luck. Rick L.