+1 on the terrible pedal position in the manual A5. I had a 2.0tdi manual as a courtesy car and the driving position felt terrible compared to the auto a3 that I had.
I've always been a die hard member of the manual brigade but my experience with a 4 pot BMW diesel manual and an A3 diesel with DSG changed that. Case would maybe be different on a bigger diesel but I can't imagine it would due to the natural characteristics of diesel engines. I'd certainly try the autos back to back against the manuals just to see. It will probably make more sense if you are going to be doing more miles and are used to free revving petrol engines.
I also think I'd try to hang about for a bit of a price drop on the e92 when the replacement surfaces.