It all depends on how well you've kept the finish on the rest of the car. Silver can be brutal, but if it's been maintained well you'll have no problem.
The "GT" on the back is just a stick on badge, but the fender emblems are located by a hole. I used Goo Gone, but I'm sure WD-40 would work well too.
I've seen MANY silver cars with the clearcoat turning to chalk / dust and / or cracking / crazing.
Any car at 11 years old out in the elements is going to show a tan line if you remove what's been covering those spots for all those years. And no, the spots won't catch up with the rest of the paint. Unless you can get a real good professional polishing job.
The paint is in pretty good shape. It may have been garage kept by the previous owners, and I can always restick them back on if it looks bad right?
Has anyone done anything creative with the side badges that have holes behind them?
One thing I had planned to do on my old Contour was replace the side badges with Volkwagen side blinkers that apparently were a perfect fit, but I never got around to it. Not so sure that would look right on a Mustang, though it does look good when people replace the Pontiac GTO side emblems with Holden Monaro side blinkers.