Ford Windstar alarm and door ajar issues.

There is a fuse for the door ajar sensor and the alarm, but it may not be advisable to pull it as it could disable other functions as well. The fuse box is located under the dashboard on the driver's side. The fuse for the door ajar sensor and the alarm is usually labeled as "door" or "security."
However, pulling the fuse for the door ajar sensor and the alarm may not completely solve the problem. If the latch is not sealing properly, the sensor may still detect an open door even if the alarm is disabled. In this case, you may need to have the latch mechanism inspected and possibly replaced.
If you do decide to pull the fuse, make sure to consult your owner's manual to ensure that you are pulling the correct fuse and that it won't affect any other important systems, such as the power windows or the radio.
If you are not comfortable with DIY repairs, it may be best to bring your vehicle to a reputable mechanic or dealership to have the issue diagnosed and repaired.

Check that the door ajar lamp lights with either door or hatch open and goes out when all closed.

more then likely it's a door ajar switch - not a sensor .
Anti-Theft- Perimeter Alarm System
The perimeter anti-theft system provides for vehicle security through an audible and visual notification if the vehicle's exterior is invaded without the system being shut off. The system self-arms when the doors, liftgate and hood are closed and the key is OFF. Any open door, hood or liftgate will prevent the system from arming. The hood ajar switch, door ajar switches and liftgate ajar switch cause these circuits to register as normally closed circuits. The vehicle security module monitors the status of the hood ajar, door ajar and liftgate ajar switches. If these circuits indicate an open entry point, the switch opens the circuit to the vehicle security module, which energizes the horn and autolamp relays (causing the horn to sound and the lights to flash). The vehicle security module turns off the anti-theft system when it receives a command through the keyless entry keypad, remote keyless entry (RKE) transmitter, or anti-theft alarm inhibit switch.
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if anti theft module not communication with scanner or diagnostic hook up then your vehicle will probably not start till thats corrected and clicking sounds like relay from security system opening up and shutting down power for starting system

anti theft light should blink every few seconds.

try disconnecting the battery for 15 minutes.

Anti-Theft-Perimeter The perimeter anti-theft system consists of the following components:

• anti-theft indicator (THEFT)
• remote anti-theft personality (RAP) module
• hood switch
• keyless entry remote transmitter
• deck lid ajar switch

NOTE: The remote entry features will not function when the ignition switch is in the RUN or ACC position.
Up to four keyless entry remote transmitters (15K601) can be programmed at one time.
The keyless entry remote transmitters :

• Are programmable.
• Must be set at the same time.
• House four buttons.
• House three buttons (Mexico Anti-Theft System only).

Programming
Refer to Section 501-14B.
Inputs and Outputs
The remote anti-theft personality (RAP) module receives input from the following components for anti-theft operation:

• Hood switch.
• Deck lid ajar switch.
• Keyless entry remote transmitter.
• Power door lock switches (LH and RH).
• Door courtesy input.

The RAP module distributes output to the following for the anti-theft system:

• Power door unlock relay.
• Power door lock relay.
• Liftgate unlock relay (Wagon)
• Park lamps relay.
• HORN relay.
• Dome lamp.
• THEFT indicator.
• Deck lid release.

Arming
The anti-theft system can be armed if:

• The ignition switch is in the OFF position.
• The panic alarm is off.
• All doors are closed.

NOTE: If a door is open, the anti-theft system is prearmed and waiting for all the doors to be closed. The THEFT indicator will remain illuminated for up to 30 minutes waiting for all the doors to be closed. If a door remains open after 30 minutes, the THEFT indicator will turn off and the system will return to a disarmed state. After all doors are closed and the 30 second prearm (continuous THEFT indicator illumination) is complete, the system is armed.
NOTE: If the theft LED does not flash after 30 seconds, check the LED FLASH PID to see if the feature is enabled.
The anti-theft system will be armed when the lock button on the keyless entry remote transmitter is pressed, all doors are closed and 30 seconds have elapsed.
When the system is armed, the THEFT indicator will flash quickly until the system is triggered or disarmed.
Disarming
NOTE: Using a key in a door lock cylinder to unlock is not a valid method of disarming the anti-theft system.
Untriggered System
NOTE: If the driver arms the system and remains in the vehicle, an untriggered system can be disarmed by turning the ignition switch to the ON position.
An untriggered alarm system can be disarmed by pressing the unlock button on the keyless entry remote transmitter.
Triggered System
NOTE: If the hood or trunk are open when the system is armed, it must be closed and opened again before it can trigger an alarm.
An armed anti-theft system can be triggered by the following conditions:
The deck lid door, liftgate, hood or any door is opened using a key, inside door handle, hood release, etc.

• The keyless entry remote transmitter can activate a panic alarm which is similar to the anti-theft alarm, but does not cause the THEFT indicator to flash.

A triggered alarm system can be disarmed by:

• Pressing the unlock or panic button on the keyless entry remote transmitter.
• Turning the ignition switch to the ON position.

Alarm State When Battery Power Is Cycled
When the RAP module is supplied power the first time at the vehicle assembly plant, the system will be in the disarmed state. The RAP module will remember whether it is armed, disarmed or triggered in its non-volatile memory. When the battery positive cable is removed and then reconnected, the system will return to the state it was in just before the battery was disconnected. If the system is in any prearm state, then the system will return to a disarmed state when the battery is disconnected and then reconnected.

take this to the dealer and have them scan the system door ajar switches, one or more is sticking, this is the problem with the alarm most likely as well, the door ajar switches (there are 6 on a 4 door) are twisted into the door latch inside the door without scanning the GEM (generic electronic module, controls locks and windows and wipers) you would have to pull all the door panels and taligate and test a each switch, a very expensive time consuming job.

Section 13-11: Anti-Theft System, Active 1998 Villager Workshop Manual DIAGNOSIS AND TESTING Inspection and Verification

1. Verify customer concern by operating the anti-theft alarm system.
   

1. Visually inspect the following components of the anti-theft alarm system:
   
   
   VISUAL INSPECTION CHART Mechanical Electrical
   • Door lock key cylinders binding
   • Loose hood anti-theft switch
   • Blown fuse(s):
     • 7.5A S.E.C.
     • 10A ELECTRON (IGN)
     • 30A PWR WDW
     • 15A HORN
   • Damaged circuit breaker #1
   • Damaged or corroded anti-theft relay
   • Broken or loose wiring
   • Damaged,loose or misaligned hood anti-theft switch
   • Damaged or loose luggage compartment lamp switch
   • Damaged or loose door courtesy lamp switch(es)
   
   

1. Verify that the following systems are operating correctly:
   
   • Horn.
   • Headlamps.
   • Instrument cluster and panel lighting.
   • Power door locks.
   • Keyless entry remote transmitter (if equipped).
   If any systems are not functioning properly, refer to the appropriate section of this service manual for diagnosis and testing before proceeding.
   

1. Check wiring harness for obvious signs of looseness, corrosion, or damage.
   

1. If the fault is not visually evident, determine the symptom and proceed to the Symptom Chart.
   

Section 13-11: Anti-Theft System, Active 1998 Windstar Workshop Manual DESCRIPTION AND OPERATION Anti-Theft Alarm System NOTE: The system immediately monitors the ignition key lock cylinder upon removal of the key from the ignition. It is not necessary to arm the system for ignition key lock monitoring.

The anti-theft alarm system:

• protects the vehicle from unauthorized entry into the passenger compartment, engine compartment and cargo area.
• monitors the status of the ignition key lock cylinder.
• is controlled by a remote anti-theft personality (RAP) module. The remote anti-theft personality module also controls the electronic door lock functions. Refer to Section 01-14B for more details.
• when armed, detects unauthorized entry into the passenger compartment by using an input from the GEM module regarding the state of the door or liftgate (open or closed).
• protects the engine compartment with a hood switch which is located on the LH cowl vent panel and is part of windshield wiper motor wiring (17A477) .
• triggers an alarm if the ignition lock cylinder is forcibly removed from the steering column.

Once triggered, the system responds by:

• flashing the low beam headlamps, the parklamps, rear lamps and the alarm indicator warning light emitting diode (LED).
• sounding the horn (13832).
• disabling the starter circuit until the system is disarmed.

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Remote Anti-Theft Personality Module

• The remote anti-theft personality module is located behind the instrument panel (04320).
• It contains a radio receiver that receives the RF signal from the keyless entry remote transmitter (15K601) through the alarm and lock system antenna (15603) and sends the appropriate command to the power door locks, the horn relay, or the generic electronic module.
• The remote anti-theft personality module is equipped with an internal backup power supply which holds the programmed code in memory in the event the vehicle battery is disconnected.

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Remote Anti-Theft Personality Module Removal

1. Disconnect battery ground cable (14301). Refer to Section 14-01 .
   

1. Remove radio. Refer to Section 15-01 .
   

1. Remove lower instrument panel center finish panel. Refer to Section 01-12 .
   

1. Lower glove box.
   

1. Remove two remote anti-theft personality module bracket retaining screws.
   

1. Disconnect electrical connectors and alarm and lock system antenna (15603).
   

1. Remove remote anti-theft personality module and bracket.
   

1. Remove remote anti-theft personality module from mounting bracket.
   

Installation

1. To install, follow removal procedure in reverse order.
   

1. Tighten remote anti-theft personality module bracket retaining screws to 6-8 Nm (54-70 lb-in).
   
   

Components The system is composed of the following components:

• remote anti-theft personality (RAP) module with integral antenna
• alarm indicator LED
• door lock cylinder switch RH, door lock cylinder switch LH
• liftgate door lock cylinder switch (220A40)
• hood switch (part of windshield wiper motor wiring (17A477))
• ignition lock anti-theft switch (19A438)

The following vehicle components are also used by the anti-theft alarm system:

• generic electronic module
• power door lock switch (14028)
• door open warning lamp switch (14018)
• autolamp relay (14N089)
• horn relay and bracket (13853) and horn (13832)
• low beam headlamps
• rear lamps (13404) and parking lamps (13200)
• starter relay
• door lock relays
• keyless entry remote transmitter (15K601)

--------------------------------
Disarming an Untriggered System NOTE: A perimeter alarm will "shut off" after 165 seconds, but the system is still triggered and is not disarmed.

An armed but untriggered perimeter anti-theft system can be disarmed by one of the following four events:

1. Unlock the doors by pressing the keyless entry remote transmitter (15K601) UNLOCK button once.
2. Unlock any door with a key.
3. Turn ignition switch to RUN or ACC.
4. The remote entry PANIC button will disarm the anti-theft system only when the perimeter alarm is triggered and sounding.

------------------------------------------------
System Triggering NOTE: Although the remote entry PANIC alarm is not associated with the monitoring of the vehicle, the user will frequently say that the theft system was triggered when actually the keyless entry remote transmitter PANIC button was inadvertently pressed. A panic alarm will not flash the THEFT indicator.

The alarm can be triggered by the following events if the system has been armed and has not been disarmed first:

• Open any door or liftgate.
• Open the hood (16612) (if the hood was open when the system was armed, it must be closed before it can trigger the alarm).
• Dislodge the ignition key lock cylinder.
• The anti-theft system may be triggered inadvertently when the module is disconnected and then reconnected. To avoid inadvertent alarm triggering, disconnect the smaller 22-way connector first.

When the system is triggered the perimeter alarm will operate as follows: The remote anti-theft personality module will pulse the following outputs at approximately 1.3 Hz, 50 percent duty cycle for two minutes 45 seconds for North America. NOTE: Other perimeter alarms can be programmed for the system.

• low beam headlamps
• parking lamps
• horn
• THEFT indicator

The perimeter alarm can be retriggered, after a perimeter alarm has sounded for 165 seconds. After a perimeter alarm has timed out, if any trigger input is first seen as normal and is then seen in its trigger state, the perimeter alarm will be retriggered. The perimeter alarm can be triggered a total of three times between an arming sequence and a disarm event. An active panic alarm will be deactivated when a perimeter alarm is triggered (a perimeter alarm overrides a panic alarm).