I modified the heck out of mine. It is only a an '09 S/E, so what the heck. It's my daily driver, and I'm having fun with it.
You are in another boat. I really think in the future those first 6400 are going to be the ones worth $$$. So if I'm in your shoes, I wouldn't modify it unless you plan to keep it for life, or don't care about resale value. If you think you might want to sell it in the future, being stock and being one of 6400 is a BIG bonus for you.