M.Y. has a write up in his signature about fixing the side molding. Or at least I thought it was him. I'll see if I can find it. I do know that the molding as a thin piece of metal in it so if you aren't careful when you pull it off, it'll bend.
Now, on to the MOD list. If it's stock and you are looking for a place to start, you can choose to follow this list. I complied this with the help of Stangnet (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) Full Exhuast (headers, hi-flo cats, catback w/ mufflers)
4) Buy a
K&N panel filter (no CAI kit required) and put it in the stock box
5) Bumped timing to 12 - 14 degrees (free mod) 10 Degrees is stock.
6) Larger MAF, TB (MAF cars from 1988 california only, 1989-1993)
7) 3G alternator upgrade / electric fan
8) Fix the weak brakes
Optional MODs:
9) Strut tower brace (necessary on Convertibles IMO)
10) Underdrive pullies (they can't be used on S/C motors and cause charging problems)
11) Weight reduction out of the nose of the car
12) Shocks/Struts and lowering springs
13) C/C plates if you lower the car
14) Short throw shifter (if you have a manual transmission)
15) 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