Allow me to add something to the mix.
I'm in a similar position in that I can freely chose among both, and I'm having a similar dilemma.
First, there's no "bad" choice. But, they are VERY different choices.
On a "daily driver" basis, the (stock) GT is simply the better car precisely BECAUSE the GT500 is SO performance oriented. Particularly with the SVTPP (which is what REALLY helps to make the GT500 a very different vehicle), the ride is MUCH firmer, bordering on harsh, and NJ winter-potholed roads (I'd never take a GT500 out of the garage between November and March) are nothing to sneeze at. The GT500 is made to be "tighter" to handle all of the additional torque and forces placed upon it.
Also, with a 3.73 Rear Axle, the 5.0 is ALMOST as quick as the GT500 with a 3.55. That's one of the reasons why the SVTPP is SO valuable (and Ford is making a ton of money by making people spend $3,500 on OTHER items just to get it). Add the Brembo brake package, and the 5.0 is an excellent stopper. The differences are really only meaningful on a track and on paper.
In favor of the 5.0 are a lot of things. First, about $15-$20K. Second, the interior is considerably more comfortable. Personally, I LOVE the Red Brick Premium interiror, especially with a white exterior. No go on Shelby for anything but black seats with inserts that match exterior stripes, and a limited palette of odd stripes if you get the SVTPP. You also get a backup camera, less "over the top" growl when other people happen to be in the car, and a front end that can be modded inexpensively to the California Special look or any variation you prefer.
If I wanted the Mustang to be a car I would drive most days, I'd choose the 5.0 hands down. It's 80-90% of the GT500 fun, and a lot of the GT500 fun is knowing that so little can keep up, not that it changes your life. If I wanted a true performance car that I could take to a track, be taught how to drive to its full potential, or wanted a potentially collectible item, the Shelby would be my clear choice. The dilemma, however, is that every mile you enjoy driving is one mile less of value to a collector.
You can upgrade almost everything but a blower in a very similar way to the GT500. I mean, the GT500 uses the GT as its platform. It may be a crystal clear choice for many, but not everyone, and certainly not for me. I have to place my order today, and I STILL haven't decided.
One other HUGE factor that nobody has mentioned are the new CAFE standards that are getting tougher each year through 2016. It's going to affect what's available, and makers are going to have to start limiting production and charging prohibitive pricing for performance vehicles that compromise economy. NOBODY can presume the 5.0 will be as powerful (or even available) in 2016.
As I try to reconcile my final choice, I'm even weighing decisions like whether or not my wife would enjoy driving the Shelby (probably not a much), or the 5.0 (very likely) simply because you have to like the Shelby's "rough and tumble" noises and sensations. And given how beautiful I think the 5.0's white/red combination happens to be, particularly with a billet grille and CS fascia, I KNOW that even behind the wheel of a GT500, if I ever saw a 5.0 in the combination I like, I couldn't help myself from envying the other driver.
And yes, there's the money. Look, I don't know you or your family, but their generosity shouldn't mean you shouldn't show enough consideration to treat their money like it was coming from your wallet. It's just good juju.
Honest to God, 3 hours from the deadline, I don't know what my final decision will be. But I DO know that there are MORE than enough reasons to choose either, even if there are very few reasons to NOT choose the other.
2013 GT500 Coupe Performance White Race Red Stripes SVT Performance Package SVT Track Package Glass Roof Electronics Package Recaro Seats Shaker Pro Car Cover
2013 GT500 Convertible Performance White Race Red Stripes SVT Performance Package Electronics Package Recaro Seats Shaker Pro Car Cover
2012 BOSS 302 Race Red White "C" Stripe Recaro Seats and Torsen Helical Differential BOSS 302 Car Cover