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I am in the process of doing some custom work to my highlander and I wanted ot know if anyone has the wiring diagram for the car for installation of an alarm and car stereo.

Also does this car have an immobilizer (encoded key)?
 

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Yes, it uses an immobilizer. Here's the wiring guide from DEI.

Remote Start/Alarm
12volts white (40A), yellow (30A) + ignition harness
Starter black/white + ignition harness
Second Starter black + ignition harness
Ignition gray + ignition harness
Second Ignition green + ignition harness
Third Ignition N/A
Accessory blue + ignition harness
Second Accessory N/A
Keysense green - ign harn or BECU, 2nd plg dwn, pin 2
Notes: Using the status output from the remote start to trigger this wire will disarm the alarm without unlocking the doors.

The BECU (Body ECU) is behind the glove box, it is the module to the right.
Power Lock see DirectFax document 1070
Notes: The driver side wires are at the driver door module in the door. They are: lock - green in pin 4, unlock - yellow in pin 14, and lock detection - brown in pin 16.

The passenger side wires are at the BECU behind the glove box, 2nd plug down from the top. They are: lock - purple in pin 8, unlock - lt. blue in pin 13, and lock detection - brown in pin 11.
Power Unlock see power lock notes
Lock Motor blue 5wi BECU, bottom plug, pin 1
Notes: The BECU (Body ECU) is behind the glove box, it is the module to the right.
Unlock Motor brown 5wi BECU, bottom plug, pin 2
Notes: The BECU (Body ECU) is behind the glove box, it is the module to the right.
Parking Lights+ white to brown + driver kick, 20 pin plug, pin 8
Parking Lights- purple - sw. or BECU, 2nd plug down, pin 18
Notes: The BECU (Body ECU) is behind the glove box, it is the module to the right.
Hazards orange - turn signal flasher left of column
Turn Signal(L) red + turn signal flasher left of column
Turn Signal(R) blue + turn signal flasher left of column
Reverse Light red/black to pink + driver kick, 14 pin plug, pin 10
Door Trigger green - ignition key cylinder illumination
Notes: Can also use the individual door trigger wires at the BECU behind the glove box. The driver door trigger is black in the 3rd plug down, pin 11. The front passenger door is lt. blue in the bottom plug, pin 16. The rear door trigger wire is lt. green in the bottom plug, pin 15. Use all three wires and diode isolate each.
Dome Supervision comes on with unlock
Trunk/Hatch Pin green - BECU, 3rd plug down, pin 6
Notes: The BECU (Body ECU) is behind the glove box, it is the module to the right.
Hood Pin green/black to white - pin switch or Theft ECU, pin 34
Notes: The Theft Deterrent ECU is behind the glove box.
Trunk/Hatch Release N/A
Power Sliding Door N/A
Factory Alarm Arm arms with lock
Factory Alarm Disarm disarms with unlock
Disarm No Unlock use key sense wire
Tachometer black ac ECM, top plug, pin 5
Notes: The ECM (Engine Control Module) is behind the glove box, it is the module to the left.

The tach wire is also found at the data link connector, pin 9, under the driver side dash.
Wait to start N/A
Brake Wire black + brake pedal switch
Parking Brake black - parking brake switch
Horn Trigger pink - column or BECU, bottom plug, pin 10
Notes: The BECU (Body ECU) is behind the glove box, it is the module to the right.
Memory Seat 1 N/A
Memory Seat 2 N/A
Memory Seat 3 N/A
Immobilizer Bypass Module: Required: Yes Type: Transponder Part #: 555U
Notes: N/A

Audio
Radio 12v blue/black + radio harness
Radio Ground brown - radio harness
Radio Ignition gray + radio harness
Radio Illumination green + radio harness
Factory Amp Turn-on purple + radio harness
Notes: If equipped, the amplifier is under the rear load floor.
Power Antenna orange + radio harness
LF Speaker +/- pink - purple +,- radio harness
RF Speaker +/- lt. green - blue +,- radio harness
LR Speaker +/- black - yellow +,- radio harness
RR Speaker +/- red - white +,- radio harness
 
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