There are about 30 kazillion C4's out there that fit 429/460's. They are behind 351/400 modified's, as they both have the same bolt pattern. For Cobras a shorter tail shaft housing can be had from old goverment mail trucks and a few other sources. A C4 can be built to take over 800 pounds of torque, runs cooler than a C6, is lighter, and takes considerably less horsepower to drive. This results in more transmitted power to the rear wheels. A short tailshaft C4 tranny could possibly leave you room in a Cobra for a Gear Venders overdrive too. (dependent on a lot of things of course)
I believe that Coan builds just about the best there is out there, but of course there are many, many others. And Coan does not come cheap. On the upside, generally C4's are just about the least expensive of all options out there, when you start compairing the parts lists, and total costs.
I've been preaching that a built C4 with a 10 inch converter is exactly the right automatic for a Cobra for a very, very long time now. Some day, maybe someone may actually do this and give testimony. Todays trannys are not the same trannys your father had in muscle cars 20 years ago.
Whatever you do though, talk it all over really well with the folks that will build any tranny you plan on using. As for me, I'm using a Glide. Good luck.
Cobrashock