I think I can help you. I just did this on mine yesterday because my clock runs a few minutes fast each month. It was somewhere bizarre - sorry I'm not near the car to be more clear. I think I picked Sound, Settings and for some odd reason, it was there, rather than in Car, Settings. NOOO - it was in Tuning - click the AM/FM button, then Settings. I've only had it for a few months, but you'd think I'd have that one figured out due to re-setting it.
You may have a coil pack going bad. They're on the front top of the engine - you'll see them if you follow the spark plug wires back. Do you have any codes from having the engine scanned? If you can get it scanned (AutoZone will do it free), post the codes up and we'll see which cylinder(s) are misfiring. From there, you can swap coilpacks around and see whether the misfires follow the packs or stay in the original cylinders. If they move, you have a bad coil pack or two. If they don't, since you've already changed plugs and wires, I'd see about having the injectors diagnosed to see if any of them are failing.
It's a BIG job involving the removal of the front of the car. If you need to change the thermostat, you may as well go ahead and do the timing service (timing belt, t-belt tensioner/relay/arm/tensioner roller, idler roller, water pump, coolant, and serpentine belt), since the front of the car comes off and the timing system must be basically removed. You can get the thermostat out without pulling the timing belt off, but you may as well do the service to avoid duplicating the labor. I changed the thermostat on my A4 two months ago (same engine you have), and the only reason I didn't do the timing system too was that I did that over the summer. Here's a couple pictures of what is involved in changing it (your A6 requires the same disassembly as my A4 - just copy and paste):
The removal necessary:
The hole in the center of the picture, behind the timing belt, where the two sections of the belt get very close, is where the thermostat sits:
I was able to change it by pulling the timing belt about halfway out off the cam sprocket on the passenger side, and then removed the two 10mm bolts that hold the coolant channeling panel over the thermostat (in the second picture, that piece is the silver metal panel that is to the left and below the hole where the thermostat sits - I put a screwdriver against it, and tapped it out of the way with a hammer).
It's a complicated job, and takes several hours if you're familiar with it. If you don't want to take this on yourself, and you're near upstate NY, reply with a comment here and let me know - I can do the job for you. If that doesn't work out, join www.audiforums.com and search out members who are local to you - one of them may be willing to work on the car with you.
Ignore that first reply. The "service" indicator on the dashboard is programmed to come on every certain number of miles (usually 5-10k, in line with typical service intervals). It's a reminder to you that you probably have some sort of inspection or periodic maintenance due. It is NOT an indicator that there is a problem with the oil or the rear brakes. If there's a failure of some sort, in a system that is monitored by the ECU, the check-engine light will illuminate. The "service" warning is simply a reminder that you should check the owner's manual to see what servicing is due at your mileage.
The thermostat is located in a housing, mounted on your engine with the top radiator hose attached. It is relatively easy to replace.
Be sure to put the new thermostat in the correct direction (notice direction of old one before taking it out). Also, be sure to clean the old gasket from the housing and be careful not to break the housing... many are cast aluminum and overtightening a bolt can easily create a headache. :o)
Hope this helps... Good luck!
Replace the internal battery in the alarm system or complete alarm unit. the random alarm is its way of telling you the battery is on its way out