Some procedure notes and disclaimers: The actual procedure is simple. The Lawyers made it hard to speak.

YOU PROCEED WITH ALL OF THIS AT YOUR OWN RISK. I am simply not to be counted on for accuracy or experience. I will try anything before paying for it from someone else, and often have to pay a mechanic PITA money to correct my mistakes. However, I do get problems solved, mainly by using lists and logic. Try it, but don't blame me if your rotors are welded on, or if the car you have isn't the exact same one I have. Think about it first, then proceed with caution. 

Rear Vibration Troubleshooting by hierarchy of cheapest and most accessible procedures: 

This procedure chart assumes that you have checked: 

The control arm bushings for degradation and cracks/ oil damage, etc. It also assumes that you have visually inspected the CV Joint-boots first for leaks, or damage, a primary indication of internal damage. These two steps may save you a couple of hundred dollars, so pay attention. 

Brakes

You should read this tech article on replacing brake pads for hints on caliper R&R, and proper brake pad replacement techniques to ferret out most minor noises which may be the cause of your problems. 

http://www.audiworld.com/tech/wheel4.shtml

Worn Tires will cause noise, so check the tread for feathering,/unusual wear, etc. This is the first step you should take a look at. Don't assume the worst, or that the solution to your problem will be throwing money at it. It however may be the solution to your mechanic's problem of how he is going to fund his 401K, leaving you poorer and wondering how it is you are going to solve that still lingering noise problem. That aside, the tires and wheels section is to tip a hat to every legitimate mechanic, (not the minimum wage wheel jockey at Sears), who made a lot of problems go away by proceeding with this type of procedure breakdown. Don't discount the tire/wheel fault diagnostic. It may just be the solution to your problem. Remember the logic of Achem's Razor, (Most solutions to problems involve the simplest explanation.)

The procedure for strut tower guide/bearings is simply labeled strut tower guide/bearing inspection. Be sure to look at this link for strut tower replacement guide : 

http://www.audiworld.com/tech/wheel14.shtml

Very well-worn strut tower bearings can cause enormous amounts of road noise, and bad handling as well. This is harder to do if you are a beginner, and maybe a good Audi mechanic might be better suited to handle this aspect of the checklist. Any other procedure should be easy enough for someone who has wrenched a few items on their own cars, such as brakes, and you will need some average metric sockets, a torque wrench, etc. to complete them. 

Serviceable or Degraded Bushings? 

From $100-499.00 parts. Labor (65 per hour)

Wheel Balance, Thrust Angle by Hunter? 

$16.00 per wheel Costco. Others will charge more and be more subjective.

Clean the inside of the wheel with warm to hot water and soap. (grease weighs something after all) 

Wheels True? 

Your used parts guy will be able to tell you / wheel repair shop. Are they elliptical or are they round? That will cause a big difference in ride, even though they may be balanced. Even a lip nougie will cause shift in rotational surface. (free).

Rotate Tires? 

This will cause the noise to subside after about 500 miles, or change pitch.  Rotation is key to tire health and noise correction. Cost: Nothing with the guy you bought the tires from originally. ($15.00 bucks is about all I'd pay otherwise.)

Check the Caliper Guide Pins 

Springiness of the pins and lube can cure sticky caliper mount action. You may need to re-grease them to retain the smooth pull action of the caliper or /rebuild the caliper. Hell, just spring the $100.00 for a new one. It works right out of the box any way. (free to $200 per axle.)

Replace Rotors

You should do this with every pad swap/brake job on later model Audi. This is because of Euro Spec disc manufacture results in thinner new discs, very little room for "resurfacing" to correct runout, grooves etc.  ($40.00 buck ea. for OEM discs through everyone but the dealer, at least on my 98 slow sedan A6 quattro). 

CV Joint Boots

($18.00 each.) Read the above notes. Link on the procedure: 

http://www.audiworld.com/tech/misc27.shtml

CV Joint Shaft Assembly

Is it true/straight? Lubed? On Quattro models you have 4 shafts, two Front, two Rear. ($100.00 or more at an independent shop).

Contact an Audi Specialist

I am sorry if you got to this point. Seems unfair. However you are probably already making this decision based on what you heard from your mechanic on that last step. At Least you won't pay an additional $600.00 for diagnostic time. 

Any work necessary beyond this point will require a skilled mechanic who is familiar with (1) Audi late model transmission and driveline problems, (2) Audis in particular. Your chevron mechanic may have a few old Mercedes in his parking lot, but that doesn't entitle him to screw with your baby. Ask on Audiworld forums for your area favorite Audi Independent/Service Shop. 

** Assuming you did this professionally the wheels would be mounted correctly, therefore the mounting issue was skipped deliberately.