This is a cut and paste from the Ford Workshop manual DVD. Unfortunately it didn't also copy the pictures which would make it easier for you to follow.
I'd think the most likely problem would be the switch on the brake pedal. I had to replace mine.
The servo is a possibility. Mine quit again and troubleshooting is pointing the finger at the servo. The servo, by the way, on my 1999 is on the passenger side fender well just behind the windshield washer tank. It will have a cable going to the throttle.
Flash code 2
Circuitry.
BPP switch. (Brake Pedal Switch)
CPP switch or jumper. (Clutch Pedal)
Speed control servo.
GO to Pinpoint Test B .
PINPOINT TEST B: FLASH CODE 2 — BRAKE PEDAL POSITION SWITCH CIRCUIT FAILURE
CONDITIONS DETAILS/RESULTS/ACTIONS
B1 CHECK THE BRAKE PEDAL POSITION (BPP) SWITCH CIRCUITRY
Speed Control Servo C171
Measure the voltage between speed control servo C171 Pin 4, Circuit 306 (TN/LB), harness side and speed control servo C171 Pin 10, Circuit 57 (BK), harness side.
Is voltage present?
Yes
GO to B7 .
No
If the vehicle is equipped with automatic transmission with high series console, GO to B5 . If the vehicle is equipped with a manual transmission or automatic transmission without high series console, GO to B2 .
B2 CHECK THE CLUTCH PEDAL POSITION (CPP) SWITCH
CPP Switch or Jumper C209
Measure the resistance between CPP switch or jumper Pin 3 (component side), and CPP switch or jumper Pin 4, (component side).
Is the resistance less than 5 ohms?
Yes
GO to B3 .
No
INSTALL a new CPP switch or jumper. TEST the system for normal operation.
B3 CHECK CIRCUIT 306 (TN/LB) FOR AN OPEN
Measure the resistance between speed control servo C171 Pin 4, Circuit 306 (TN/LB), harness side and CPP switch or jumper C209 Pin 3, Circuit 306 (TN/LB), harness side.
Is the resistance less than 5 ohms?
Yes
GO to B4 .
No
REPAIR the circuit. TEST the system for normal operation.
B4 CHECK CIRCUIT 810 (RD/LG) FOR AN OPEN
BPP Switch C224
Measure the resistance between CPP switch or jumper C209 Pin 4, Circuit 810 (RD/LG), harness side and BPP switch C224 Pin 2, Circuit 810 (RD/LG), harness side.
Is the resistance less than 5 ohms?
Yes
GO to B6 .
No
REPAIR the circuit. TEST the system for normal operation.
B5 CHECK CIRCUIT 810 (RD/LG) AND CIRCUIT 306 (TN/LB) FOR AN OPEN
BPP Switch C224
Measure the resistance between speed control servo C171 Pin 4, Circuit 306 (TN/LB), harness side and BPP switch C224 Pin 2, Circuit 810 (RD/LG), harness side.
Is the resistance less than 5 ohms?
Yes
GO to B6 .
No
REPAIR Circuit 810 (RD/LG) or Circuit 306 (TN/LB). TEST the system for normal operation.
B6 CHECK CIRCUIT 57 (BK) AT BPP SWITCH
Measure the resistance between BPP switch C224 Pin 1, Circuit 57 (BK), harness side and ground.
Is the resistance less than 5 ohms?
Yes
INSTALL a new BPP switch; REFER to Section 417-01 . TEST the system for normal operation.
No
REPAIR Circuit 57 (BK). TEST the system for normal operation.
B7 CHECK THE BPP SWITCH
BPP Switch C224
Measure the voltage between speed control servo C171 Pin 4, Circuit 306 (TN/LB), harness side and speed control servo C171 Pin 10, Circuit 57 (BK), harness side.
Is voltage present?
Yes
If the vehicle is equipped with automatic transmission with high series console, REPAIR Circuit 810 (RD/LG) or Circuit 306 (TN/LB). If the vehicle is equipped with a manual transmission or automatic transmission without high series console, GO to B8 .
No
INSTALL a new BPP switch; REFER to Section 417-01 . TEST the system for normal operation.
B8 CHECK CIRCUIT 306 (TN/LB) FOR SHORT TO POWER
CPP Switch or Jumper C209
Measure the voltage between speed control servo C171 Pin 4, Circuit 306 (TN/LB), harness side and speed control servo C171 Pin 10, Circuit 57 (BK), harness side.
Is voltage present?
Yes
REPAIR Circuit 810 (RD/LG). TEST the system for normal operation.
No
REPAIR Circuit 306 (TN/LB). TEST the system for normal operation.