as far as bolt ons.......
CAI (Densecharger/Demolet, anything plastic)
X-pipe and Catback (register at mustangexhaust.com to hear one you like)
Underdrives (Steedas only, piggyback style ones like march are worthless)
Handheld Tuner (SCT XCal2 or Diablo Predator work fine, install their tune then add timing and take away fuel till you start to ping at wot, then you have just found the edge, then bring back the timing a degree or two and add in some fuel for a safe tune)
Shifter (Steeda Tri-Ax, MGW, Etc all work well, anythings better than stock)
Rear Gears (3.73's if going forced induction later, 4.10's if staying naturally aspirated, 3.90's if you dont know yet and you can get the best of both worlds later. oh and a traction lock rebuild or better yet, a whole new unit (31spline eaton posi with some 31spline axles will make for a stout rear end)
throttle body and plenum combo (stay away from mac)
thats about it before you start going into 1000$+ mods like cams, heads, nitrous
, forced induction, forged internals, etc.