Your 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 and should be the first modification
3) Buy a K&N panel filter (no CAI kit required) and put it in the stock box
4) Exhuast (headers, hi-flo cats, mufflers)
5) 3G alternator upgrade / electric fan
6) Larger MAF, TB (MAF cars from 1988 california only, 1989-1993)
7) Fix the weak brakes
8) Bumped timing (free mod) 10 Degrees is stock.
After those, it's pretty much up to you. There are plenty of Super Chargers or Heads, Cam and Intake packages to choose from.
Also, don't forget about the basic tune up which should include:
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
3) Oil filter: Motorcraft or equivalent (not FRAM)
4) Air filter: see above
5) Plug wires: Ford Motorsport (FRPP) 9mm units are great
6) Cap / Rotor
7) Oxygen sensors
Edit: This just covers the basics of things that you will need to upgrade / replace in your quest to reach a power level that you are happy with. FRPP now sells the Powerdyne 6PSI kit for 1,600.00 but without all of the supporting mods first, you won't see the full potential of the kit.