I too was aware of previous issues as a colleague had similar trouble on pre 2009 models, but was assured that these were no longer a risk by the dealership, when I ordered it in 2011.
The parts (fitted) were £3400 opposed to the gearbox (fitted) which was £7600
Audi initially offered 70% discount, we finally settled with me having to fund £1000 + VAT.
I must admit it has made me wary of purchasing another 2.0 TDI Auto, even though I am a very keen VAG user this being my 7th vehicle !
I hope this helps, but not sure what you can do to reduce the risk, as my car is not driven hard and is well serviced. The dealer stated is is very uncommon but it was not a particularly hard negotiation for the discount, which makes me think it could be otherwise ?