I agree that one should wait for the hype to die down and avoid these issues. However, I ordered a '99 Mustang when they were the "new" body style and did not experience this problem. I then ordered another in 2000 due to my positive experiences.
This said, the dealer I work with has several GTs on the lot, but the are all autos. Is something wrong with the new manual 6 speed transmissions? I have yet to see one anywhere, on a lot or in person otherwise.
One more thing. To the OP. I would not take a GT500 that has sat outside that long. When I was looking for one, I immediately walked away if the car was sitting outside on the lot, as opposed to the showroom. If I'm spending that kind of cash, it will be to my liking or it won't happen.