Parts or components should not be replaced with reference to only a P3999 DTC. The vehicle service manual should be consulted for more information on possible causes of the fault, along with required testing.
P3999 OBDII Repair :P3999 code shows that location the body harness connector, located in and around the left hand kick panel area or inside the IP (consult a shop manual for location). Water can leak into the connector from clogged sunroof drains, A-pillar leaks, or windshield or cowling leaks.
The crank but won't start condition, along with the trouble codes may make you think you've got a PATS anti-theft system problem. However, Ford reports that these codes are all related to software bugs. The only way around the problem is to reprogram the PCM with the latest software.
Gasoline engines use spark plugs to cause an explosion of fuel within the cylinder. In a properly timed engine, this explosion occurs at the proper moment to send the piston to the bottom of the cylinder and provide power to the drive shaft. If the plug wires are out of sequence, the explosion occurs at the wrong time. The improper timing of the explosion sometimes pushes the cylinder the wrong direction or interferes with the turning of the crank. As a result, the engine stutters or backfires, if it runs at all.
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