I'm actually confronting the same choice - with the GT500. And it's always kept me away from convertibles, particularly for any manner of high(er) performance vehicle, because of the inherent penalties to handling that are usually just too difficult to overcome or the other compromises that often have to be made in order to accommodate the convertible.
For example, there's no 3:55 or 3:73 axle option on the GT Convertible - at ANY price. It was ONLY the fact that Ford seems to have made some significant improvements specific to the 2011 GT500 Convertible that make it as rigid as the 2010 Coupe - with only about 150lb of weight penalty - and makes every performance option available that can also be had in the Coupe that made me consider it.
You DO have another option, and that's the Glass Roof. Even more than allowing coupe owners to let a little sunlight in, it allows V6 and GT owners to do it without giving-up any of the best performance features.
At the end of the day, there's really NO "bad" decision to make, unless you have a very specific scope of use in mind, like tracking your car which would clearly make the coupe the better choice. Otherwise it's really a toss-up between priorities, but there's just no denying the Convertible is capable of one thing the Coupe just can't do - at any price or speed.
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