GT40, Cobra, or Daytona... they all take the same Ford lumps, so maintenance is nil and parts cost a dollar and a half from the NAPA store down the street.
Daytona and Cobra use brandy-new Tremec transmissions, and they are bulletproof, cheap, and sold at the local 7-11.
For the GT40's transaxle, you'll be waiting for the new ZFQ from Quaife, or waiting for an RBT... you'll be waiting, at least a little bit, no matter what.
You really should at least sit in a GT40 before committing to taking it on any kind of non-recreational drive. It is loud, hot, uncomfortable, has zero rear visibility, windows that don't open (unless you remove them completely), and you'll be rubbing shoulders with any terrified passengers who dare to ride with you. However, if you are unlucky enough to be next to a big SUV on the 405, don't worry... if he doesn't see you before he changes lanes (which he won't), the GT40 is so low that you'll fit neatly underneath his chassis. Oh, and you can't see traffic lights unless you're five car lengths back from the intersection, or have a periscope! As to ground clearance, an Apple iPhone won't fit underneath the thing standing up... a soda can ON ITS SIDE will barely make it... you'd be lucky to not scrape on the Bott's Dots on the freeway! We are talking really, really, unbelievably low ground clearance. I have never seen another street-legal car with so little clearance. Four inches from street to floorpan, plus the huge front overhang, equals lots of scraping sounds all day long. If you're taller than 5'9", plan on taking yoga classes to figure out how to get into the thing and shut the door without bashing your head.
Jeff B's dad was kind enough to take me out for a few laps in his SPF GT40 a few weeks ago at Firebird West, and that beast pulls like a freight train, but they needed special methods to get it on and off the toy hauler, whereas the new Ford GT just rolled on and off with no problems (and that beast is looooow by any standards).
All of this adds up to make the choice easy, for me at least... GT40 all the way!!!!
Seriously though, if you're in SD, take a run over to VIP Classics and have a sit in a CAV GT, or, better yet, haul on up to Superformance/Hillbank in Irvine, where you can compare the GT40, Cobra, AND Daytona side by side in the same room... click this link for a recent photo of their new showroom:
Shelby Heaven: Superformance opens new showroom - Autoblog
For the CAV GT40s in SD, click on this one:
Classic cars for sale - European, American antique and Vintage automobiles
And for the Superformance showroom in Irvine, click on:
Hillbank Motor Corporation
A drive up to Hillbank is probably the best bet, you'll be able to sit in and directly compare three of your four options... Good luck making a choice, it won't be easy!
(BTW: What about an 05/06 Ford GT or the new Audi R8?)