Okay, let me see if I can address everyone.
NOTE: I have since done more research and found that it is still covered under the powertrain. So, before it hits 60k miles, I'll just get rid of it and get another one or drive the GT500 sitting in the garage not being driven. Which is what I should have done to start with.
The car is completely stock with the exception of resonator deletes.
I have spoken with numerous dealerships. I spoke with the dealership I bought it from as well as my local, trusted dealership who I've been dealing with for years. I have an awesome service rep there. When I was told it wasn't going to be covered under warranty, I was speaking with another young man who I have since found out is very new. When I actually got in touch with the rep I've been dealing with for a while, he straightened it out.
Now, this is NOT an unknown problem. If you look, there are a lot of people having this issue. I found at least 20 forum entries on other mustang sites stating the same issues I'm having. I realize in the grand scheme of things, 20 entries is nothing, but who knows how many others are out there. The car lurches, almost violently, from park or reverse to drive. I've already been through this once with it so I know the reflash is what it needs. My service rep agrees. It's not a 5 minute job. The last time I had it done it took about 45 minutes. From what I have read about it, it's just like any other computer, nothing happens quickly.
The car has 36k miles on it. It's out of warranty with the exception of the powertrain.
I did not initiate the challenge with the Cobra, HE did, but I'll be damned if I'm not going to accept the challenge. So I guess I'm an a$$hole, and I'm okay with that.
So, all in all, this is going to work out. Like I said, I'll keep it until it gets close to 60k, then move on. It's just an inconvenience to have to get it to the dealership, and find another car to drive, etc.. Right now the GT500 is in pieces because my husband decided to do a full detail, and is now working 70 or 80 hours a week so hasn't had time to finish it up.
Thanks everyone for your responses. Like I said, it looks like it's all going to work out now.