Engine starts for 3 seconds and then shuts down, radio,locks,trunk release,interior lights do not work, clock/radio display shows time but nothing from radio

You probably fried a control module , It doesn't take long ! Would need to hook up a professional scan tool that can communicate with all the modules . Check codes the BCM - body control system . Without testing we would only be guessing . Your best bet would be to take it to a qualified repair shop . Your looking at major bucks . I have worked at cadillac an have see this before ! Control Module Diagnostics with John Anello
Sorry but there is no way you'll be able to fix this !
This vehicle has electronic components which the service technician controls in order to provide valuable self-diagnostic information. These components are part of an electrical network that controls various engine subsystems and various body subsystems. A description of each of these subsystems is in the appropriate subsection of this service manual. These major components that compromise the computer system monitor the system sensors and the system switches. These components are the following:
• The powertrain control module (PCM)
• The instrument cluster
• The air controller module (ACM)
• The sensing and diagnostic module (SDM)
• The electronic brake and traction control module (EBTCM)
• The continuously variable road sensing suspension module (CVRSS)
• The body control module (PZM)
• The integrated radio controller (IRC)
• The remote function actuator (RFA)
• The climate control panel (CCP)
• The cellular telephone (PHN)
System Functions
The body control module (PZM) performs the following functions:
• HVAC afterblow control
• Battery guard
• Door lock and unlock
• Fuel level
• Retained accessory power (RAP)
• Theft deterrent
• Exterior lighting control
• Interior lighting control
• Trunk release
• Time of day for the radio display
• Rear defogger
• Fuel door release
• Vehicle personalization
For more information about these functions refer to the appropriate sections.

On my 2003 ST T30 X-Trail the radio is called SY702, this is printed to the right hand side of the number 6 button.
Turn the ignition to ACC, turning the radio on.
Press and hold both 'AUDIO' and 'AS' simultaneously for 3 seconds. Clock display will start flashing.
Release 'AUDIO' and 'AS'
'1' button advances the hours.
'2' button advances the minutes.
When you're finished setting the clock, press 'AUDIO' to lock the time in. Ant :)

On my 2003 ST T30 X-Trail the radio is called SY702, this is printed to the right hand side of the number 6 button.
Turn the ignition to ACC, turning the radio on.
Press and hold both 'AUDIO' and 'AS' simultaneously for 3 seconds. Clock display will start flashing.
Release 'AUDIO' and 'AS'
'1' button advances the hours.
'2' button advances the minutes.
When you're finished setting the clock, press 'AUDIO' to lock the time in. Ant :)

YES THE ALTENATOR

You will need your 4 digit radio code. Sometimes you can find a sticker in the trunk next to your spare or in the glovebox. Otherwise you have to pull your radio for the serial number and call Audi for the code. I just used these instructions found on Fixya:
Turn on radio - the word SAFE will appear in the display. Press th P.SCAN and RBDS buttons simultaneously and hold them down until "1000" lights up in the display.Release buttons.Do not, under no circumtances, continue holding them down or press them once again. This will cause the radio to consider the number 1000 to be the input code.Use station buttons 1,2,3,and 4 to enter the code number on your Radio Card. Use the button 1 to enter the first number 2 for the second number 3 for the third number and 4 for the last number.Once you have entered the code and it shows on the display,press the P.SCAN and RBDS buttons down again simultaneously and hold them down until the word SAFE appears in the display.Release buttons.
You have three tries to enter the code correctly. If you do not, you will be locked out for at least an hour of car operation time. Good luck.

Yes there is a fuse for the trunk opener.also,do you have a valet switch to shut it off?

You shorted something out. Check all fuses and relays. I think you blew a relay not a fuse.

Telephone: Fax: VAT Registration No.:
Infrared remote control
NOTE: Infrared emitter can be seen at front edge of key.
System operation
Switch ignition ON. Ensure clock LED illuminates for 3-5 seconds. Pressing key lock button once activates central locking and alarm. Pressing key lock button twice within 3 seconds activates double locking system.
Programming
When
Key batteries completely discharged. Key batteries not replaced within 15 seconds. Key added or replaced. System malfunction.
How
Obtain all keys fitted with remote control. Turn ignition switch to position I. Wait approximately 10 seconds. Ensure clock LED illuminates.
NOTE: LED illuminates for approximately 5 seconds.
Switch ignition OFF and remove key, while LED illuminated. Programming mode activated for approximately 20 seconds (LED illuminated). Proceed as follows: Point key at receiver (located near interior lamp). Press and hold unlock button Fig. 1 [1]. After approximately 1 second key LED will flash once [3]. Press lock button 3 times Fig. 1 [2]. Release unlock button Fig. 1 [1]. Continue to point key at receiver until LEDs in clock and key have flashed 5 times. Ensure LED remains illuminated. Repeat above procedure within 20 seconds to program remaining keys. To exit programming mode and extinguish clock LED: Switch ignition ON and OFF. Wait approximately 20 seconds.
NOTE: A maximum of 4 keys can be programmed. Fig. 1
Radio frequency remote control
System operation
Switch ignition ON. Ensure clock LED illuminates for 3-5 seconds.


Pressing tailgate release button twice within 3 seconds unlocks the tailgate - if fitted. Pressing key lock button once activates central locking and alarm. Pressing key lock button twice within 3 seconds activates double locking system. Interior lamp illuminates when disarming system.
Programming
When
Key added or replaced. System malfunction.
How
Obtain all keys fitted with remote control. Fasten seat belts and close all doors. From position I, turn ignition switch as follows: To position II. To position I. To position II. To position I. To position II. To position I. Programming mode activated for approximately 20 seconds. LED or fog lamps ON warning lamp illuminates (some models) or the system will emit an acoustic signal to indicate start of programming mode. Proceed as follows: Type 1: Press and hold unlock button Fig. 1 [1]. Type 2: Press unlock button Fig. 2 [2]. Ensure clock LED or fog lamps ON warning lamp flashes (some models) or wait for acoustic signal (indicates correct programming). Wait 2 seconds. Repeat above procedure within 20 seconds to program remaining keys. To exit programming mode: Switch ignition ON. Wait 20 seconds.
NOTE: A maximum of 4 keys can be programmed.

There is most likely a fault in the system and it will have to be reapired by certified tech

please have the door lock check out!- that is a mechanical problem in the lock!