How to reset my factory car alarm in a 1999 mercury cougar v4 2.0? thanks

1999 cougar. before they tell me I need a fuel pump I want to be SURE the anti theft system has not shut off the fuel to the engine.
how do I confirm that?

Passive Anti - Theft System (PATS)
The Passive Anti-Theft System (PATS) is fully passive in operation and requires no special procedures by the driver to arm or disarm the system. It is invisible to normal scrutiny and is operated by a miniature transponder within the key body. The transponder communicates with the powertrain control module through a transceiver mounted around the ignition switch lock barrel. The PATS functionality is incorporated within the powertrain control module.
PATS may be identified by a larger than normal sized ignition key. A larger sized ignition key indicates the presence of the transponder that controls the system.
The transponder code reading is carried out when the key, having been inserted into the ignition lock barrel, is turned from position 0'' to position II'' to crank the engine. If the PCM receives the correct code, the engine will start. If the PCM receives either no code or an incorrect code the engine will not crank and PATS remains armed and the engine immobilised.
Anti-Theft Indicator
Whenever the ignition is switched on the anti - theft indicator will remain on for three seconds while the system reads the ignition key code.
The anti - theft indicator will flash rapidly or glow continuously after the initial three seconds to indicate the PATS has immobilised the vehicle.
For additional information on the PATS fault codes, refer to the Diagnosis and Testing section

Passive Anti - Theft System (PATS)
The Passive Anti-Theft System (PATS) is fully passive in operation and requires no special procedures by the driver to arm or disarm the system. It is invisible to normal scrutiny and is operated by a miniature transponder within the key body. The transponder communicates with the powertrain control module through a transceiver mounted around the ignition switch lock barrel. The PATS functionality is incorporated within the powertrain control module.
PATS may be identified by a larger than normal sized ignition key. A larger sized ignition key indicates the presence of the transponder that controls the system.
The transponder code reading is carried out when the key, having been inserted into the ignition lock barrel, is turned from position 0'' to position II'' to crank the engine. If the PCM receives the correct code, the engine will start. If the PCM receives either no code or an incorrect code the engine will not crank and PATS remains armed and the engine immobilised.
Anti-Theft Indicator
Whenever the ignition is switched on the anti - theft indicator will remain on for three seconds while the system reads the ignition key code.
The anti - theft indicator will flash rapidly or glow continuously after the initial three seconds to indicate the PATS has immobilised the vehicle.
For additional information on the PATS fault codes, refer to the Diagnosis and Testing section

Principles of Operations
The passive anti - theft system (PATS), also known as SecuriLock, uses radio frequency identification technology to deter a driveway theft. This system is known as SecuriLock in North America, Safeguard in the U.K., and PATS in Continental Europe. Passive means that it does not require any activity from the user.
The PATS uses a specially encoded ignition key. Each encoded ignition key contains a permanently installed electronic device called a transponder. Each transponder contains a unique electronic identification code out of over four quadrillion combinations.
Each encoded ignition key must be programmed into the vehicle's powertrain control module (PCM) before it can be used to start the engine. There are special diagnostic repair procedures outlined in this manual that must be performed if an encoded ignition key needs to be replaced.
The transceiver module communicates with the encoded ignition key. This module is located behind the steering column shroud and contains an antenna connected to a small electronics module. During each vehicle start sequence, the transceiver module reads the encoded ignition key identification code and sends data to the PCM.
The control functions are contained in the PCM. This module performs all of the PATS functions, such as receiving the identification code from the encoded ignition key and controlling engine enable. The PCM initiates the key interrogation sequence when the vehicle ignition switch is turned to RUN or START.
All elements of the PATS must be functional before the engine is allowed to start. If any of the components are not working properly, the vehicle will not start.
The PATS uses a visual theft indicator. This indicator will prove out for three seconds when the ignition switch is turned to RUN or START under normal operation. If there is a PATS problem, this indicator will either flash rapidly or glow steadily when the ignition switch is turned to RUN or START. The PATS system also flashes the theft indicator every two seconds at ignition OFF to act as a visual deterrent.
The PATS will be activated and will disable the vehicle from starting if there is a:

• Damaged encoded ignition key
• Unprogrammed key
• Non - encoded key (key has no electronics)
• Damaged wiring
• Damaged transceiver

I got in a wreck in a 2000 Mercury Cougar and I had to replace the hood. The replacement hood does not compress the hood alarm switch all the way down causing the alarm to sound. How do I fix this problem?