Most Cobras were 289s, and all of the Cobras that established that car as a racing legend were 289s. The Cobra that is famous with most people, however, is the "427." Oddly enough, it turns out that very few Cobras actually had 427s in them -- even those that had the 427 body style (big fender flares is the most obvious trait) and 427 badges. 427s were in short supply, so Shelby sent most so-called "427" Cobras out the door equipped with 428s.

The reason that lots of Cobra replica builders like the 406 is that it is in the same family as the 427, looks just like a 427 externally, and has very similar performance, all at a fraction of the cost. You can build a 406 from almost any late FE block just by putting a 390 crankshaft in and boring it out to 4.13". It has the same stroke as the 427, of course, so all you're giving up is a tenth of an inch of bore diameter, which amount to 19 cubic inches (the "427" really displaced only 425 cubic inches).

Of course, you could just put in a 390, but "406" sounds cooler. You could also put in a 428, which would be more technically correct than a 390 or a 406, but they're more expensive and the longer stroke isn't as well suited to the kind of driving that a Cobra was really meant for.

 

I just ran some numbers through Desktop Dyno for the he!! of it. I used the specs for how I would build a Cobra replica motor. For a 406 (4.13 bore x 3.784 stroke), DD showed peaks of 535 hp @ 6500, and 501 lb-ft @ 5000. Converting it to a 427 (4.23 bore x 3.784 stroke) and changing nothing else, DD showed peaks of 536 hp @ 6000 and 517 lb-ft at 5000.

In other words, the 406 gives up just one pony to the 427 (535 for the 406 to 536 for the 427). The 427 hits its power peak 500 rpm lower, however, and has a torque advantage of roughly 3% below 5000 rpm.

If I was building a motor that would really be raced, I would be inclined to spend the extra $5-10 thousand or so to build a real 427 instead of converting a 360 to a 406. The reason has less to do with power than with durability. The 427 blocks are high nickel nodular iron with four bolt caps. They are stiffer and more likely to hold together when run for long periods at 6000 rpm. For a Cobra replica I just intend to cruise in with occasional bouts of putting the hammer down, I'll save the money and build the 406.

Incidentally, someone suggested stroking a 427 with a 410/428 crank, and said it would yield 454 cubic inches. Actually, it would yield 447. More importantly, I don't see the point. The 427 was designed to be a high revving race motor. A long stroke would only increase rotating mass and rod angularity, which decreases acceleration and leads to all sorts of other problems at high rpms. Bad idea. Besides, 427's are too rare and expensive to be molested like that.