The OBDII port will be found on the driver's side under the dash. It's a black D-shaped connector. Plug your scan tool into this and turn the ignition key to the "on" position without starting the vehicle. Then read any diagnostic codes. If you see a P1000 do not be alarmed. This code will appear any time the battery has been disconnected, or whenever you clear trouble codes. It simply means the PCM has not yet completed all it's emissions drive cycle tests since the last time codes have been cleared. You cannot clear this code, you must drive the vehicle through Ford's recommended drive cycles for it to clear on it's own.

Code Classifications:
P0xxx - standardized powertrain codes
P1xxx - Ford specific powertrain codes. Other manufactures use these codes as well, but they are specific to the manufacturer and not standardized.
Bxxxx - body codes
Cxxxx - chassis codes
Uxxxx - reserved for future systems