Im not really good on Mustangs yet, but first I would say get either new dual exhaust (flowmasters, magnaflow etc.) depends on the taste of sound you like, then I believe you can get a cold air intake, or you can get both.
If anything I said is wrong, someone correct me.
The cool thing is I have the same car and model as you, but its still stock, so im gonna get the Flowmaster 40's. As my first upgrade, then ill get the intake.