I had a 96' WS6 TA that was only a few months old that started to do the samething. Took it to the dealer and they couldn't find any problems, but it would still misfire around 3000 rpm. I ended up replacing the plug wires and the problem was solved. The only explaination I could come up with was that I had one wire with a break in it and only when the turbulence in the engine compartment was enough to move the wire around, causing a gap in the break, did it misfire.
When I was trouble shooting, I figured the plug wires were a cheap place to start and a good thing to rule out initially.
But to tell you the truth, I haven't been in the engine bay enough to remember if the new Stangs even have wires or the pack plugs right on to the spark plugs.