Having been a fan of Ford, and the Shelby Cobra in particular, since I was a kid( 1960's!!!) I'm seeing alot of truth mixed with some missinformation, here are the facts. Carroll Shelby was a famous racing driver during the 1950's racing for many great European teams of the time, including Maserati, and won Le Mans in 1959. He retired the following year due to heart problems, and admitted later that this problem existed before then and often chewed nitro pills while racing!
He had approached Ferrari to put togther a team to race in America, but was told by Enzo Ferrari himself that their were no good drivers in America, and that racing in America was unimportant. This Angered Shelby and he began calling people he new within the American auto industry to try and build a car that he could use to beat Ferrari at their own game. Lee Iacocca offered to back him by providing money and engines, it was AFTER this that he started looking for a car to put these engines in. AC cars of England was making a car known as the Ace, but had lost their original engine supplier, when Shelby found out about this, he had one Ace shipped to America for his team to play with. This first car was outfitted with a 260ci V8 ( the 289ci engine was not manufactured by Ford until 2 years later) and this was the car shown and test driven by the various car magazines of the day. They only had one car during the first 6 months that this was going on, and painted it different colors each time they took it to a new magazine to make it appear they had more! ( God bless American ingenuity!)
The first production cars, and race cars, had 260ci V-8's, it wasn't till the third year of Cobra production that they began to use the 289. Even with the small engine, they were very fast and won most races they were entered in in the US, but were not campained overseas by Shelby until the creation of the 289 FIA car in 1964. This model used a newly designed suspension, created by Shelby's team, and was the first car NOT to use the original AC body, but still retained most of the chassis. Production 289 Cobra's were still using the original AC body and chassis until the end of their production. The FIA Cobra's were to drag limited on topend speed to win many of the races in Europe, so Shelby created the Cobra Daytona coupe in 1965, which they used to win the FIA World championship in Europe that same year. This car also used a 289ci V-8.
That same year they began work on a new Cobra, using the new Ford 427ci "side oiler" motor, this motor was originally designed for NASCAR racing, which made huge power and was designed for hours of running flat out in a 3500lb NASCAR racer, and would prove extremely reliable in the light weight Cobra. The 427 Cobra did not use any parts from the original AC car, not even the bodywork ( this was also the same time that AC cars went out of business) and was described br Carroll himself as " the ugliest damn car I've ever seen" the first time he saw it. Their were 2 versions of this car, the production version using the 427 motor and a single 4-barrel carb, and the 427 S/C using the same engine but with 2 4-barrel carbs, an oil cooler, larger radiator, and stiffer springs. The S/C was sold to those who wanted a car they could race right out of the box.
The "special" car that was mentioned by Elduchey was called the Super Cobra, and their were only 2 of these cars ever made. they featured both a chin and rear spoiler and a larger hood scoop. The scoop was enlarged to accomadate 2 Paxton Superchargers ( forerunner of the Vortec) one feeding each 4-barrel carb! no documented testing was ever done on either of these 2 cars, but they were believed to make more than 800hp. One car was given to one of Shelby's designers ( I don't remember his name, but I do remember that he died when he crashed the car several years late) and the other WAS given to Bill Cosby, which he only drove once and gave it away. Cosby talked about this car on one of his comedy albums, the album is titled 200M.P.H. and can still be found on cassette tape, I'm not sure if it has ever been transferred to CD. This car has long been searched for, but so far has never been found, if it ever turns up it will be the most valuable Cobra ever made.
And that's the story ( excluding the Shelby Mustangs and GT 40 which Shelby was also working with at the same time! But that's another story ) one other thing that was mentioned a couple of times was about the "AC" version of the Cobra, this never happened, AC cars never sold any Cobra, not even the original 260 cars, the only reasons I can think of for GT4 to have them listed this way was so they could be used in the Euro cup races, and to allow more color choices since these are listed as 427's and not 427 S/C's, this stems from the fact that all 427 S/C's ever built were blue with white stripes.
For more on Carroll Shelby, and a complete timeline of his racing and car making years, check out his web site.
http://www.carrollshelby.com/about.htm