Corey,
I assumed that you would have cleared the codes after having replaced a sensor, other component, or fixed a wire or connection, in the engine control system.
So, for the less experienced, clear the codes after any repair to the electronic engine control system. Then test drive the vehicle and re-check the codes in order to determine if the repair solved the problem.
The codes will eventually clear themselves after so many "key starts", but some of the codes will take as many as 50 key starts to clear (some more).
I agree with Scott, if you have a plug wire that is arcing you need a new set of wires. If you grab that puppy and you are grounded you will never forget it!!! eek!
Fordparts on line - Autolite plug wires for the SHO about $85 plus S/H. Replace the plugs also. If the wires are that bad the plugs are most likely fouled. Put anti-sieze compound on the threads of the plugs, and USE A TORQUE WRENCH TO INSTALL THE PLUGS. rangerj