This list covers all of the basic things that should be looked at / replaced or repaired so you get the most enjoyment out of your car. Some of this stuff is already done on your car so you will have to pick and choose.(Go STANGNET!).
First mods should be as follows (my take):
In order of Priority
1) Subframe connectors (SFC's) full length ones are prefered for a stiff chasis
2) Gears: 3.73:1 or 4.10:1 seem to be the popular choices
3) For AOD people: Get a higher stall converter and a shift kit! (don't forget theTranny cooler)
4) Full Exhuast (headers, hi-flo cats, catback w/ mufflers)
5) Buy a K&N panel filter (no CAI kit required) and put it in the stock box
6) Bumped timing to 12 - 14 degrees (free mod) 10 Degrees is stock.
7) Larger MAF, TB (MAF cars from 1988 california only, 1989-1993)
8) Better Intake Manifold or a Ported one
9) 3G alternator upgrade / electric fan
10) Fix the stock brakes.
Optional MODs:
11) Strut tower brace (necessary on Convertibles IMO)
12) Underdrive pullies (they can't be used on S/C motors and cause charging problems)
13) Weight reduction out of the nose of the car
14) Shocks/Struts and lowering springs
15) C/C plates if you lower the car
16) Short throw shifter (if you have a manual transmission)
17) Cleaning or replacing all of the sensors (TPS, IAC, etc. - not a mod but it helps)
After those basic mods it will be pretty much up to you to pick a final direction for your car. There are plenty of Super Chargers or H/C/I [Heads, Cam and Intake] packages to choose from to really wake up the car.
Also, don't forget about the basic tune up
1) Changing all of the fluids (oil, coolant, trans, rear end, brake and some of the power steering)
2) Plugs: (non-platnum type) Autolite or Motorcraft are prefered
3) Oil filter: Motorcraft or equivalent (not FRAM)
4) Air filter: see first mods item #4
5) Plug wires: Ford Motorsport (FRPP) 9mm units are great
6) Cap / Rotor
7) Oxygen sensors
Edit: Updated the list...
