The rear derailleur is dead on; I was very concerned about tossing $500 worth of derailleurs in the trash when I had them both apart and was drilling/cutting on things. However, once it was done I was very pleased with the finished part. A medium length 11s cage would be best for a 53/39 with a 12-29 cassette, even though they say it will 'work'.
I am also pretty happy if I'm only getting 3-4 gears that rub the derailleur when in low-low gearing. For now, I have the cable adjusted so that I can quiet it down on the fly. In Dallas, we don't use anything but the 53t ring anyhow. I set the bike up to handle the 39/53 with no noise in any combination of gears.
I do get chain ring rub on my Ridley, mostly because the rings I'm running (55/44 elliptical) With the stock gears (39/53, I get no rubs) Of course, this is outside of SRAM's design, so I expect it to not be perfect.