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Try unhooking your central locking pump in the trunk. Then see what happens. I saw a post not to long ago with someone who purchased a car with the CLP disconnected. When he reconnected it, the alarm would go off etc. You could give that a try to start. The person who posted the thread didn't have all the problems you are having, but its worth a shot.

As for the bump, it could be the rear diff bushings, engine mounts, snub mount or tranny mounts. Or a combination of those things.

 

Before getting your hands dirty, get your ecu scanned for soft codes related to the central locking/immo system.

 

it sounds like something to do with your alarm not turning off. when the alarm is (stuck) on, your window and lock buttons on your door will not work, and obviously your marker lights will flash when the alarm is going off.

 

if all that produces no results start with the wiring leading into the trunk from the car.

 

Thats sucks. I believe it's going to be a dealer-only item. Give your local dealer a call with your VIN and see what they say. You can scan junk yards too, but it's not uncommon for the alarm unit to fail in an older A4.

And fix your water leak before you replace any expensive parts!.

 

i believe there's a DIY someplace for doin that. Or at least a thread or two. I remember reading about that a while back. try searching for it.