I had a similar problem last month, and yes the dealer replaced the whole box. Last week I had the turbo unit replaced too, I've been told on another forum that turbo's tend to go from about 70,000 miles on the 3.0d.
Sorry I can't give you any idea of costs as all mine was carried out under warranty
To see my thread click HERE
I hope you get it sorted to your satisfaction, I must admit mine has never run better since all this work
but then again it should do!