I forgot to mention that the front derailleur is very tight against the fenders (both the SKS P50s and the Cascadia 29ers), but I don't notice any shifting problems. The old fenders got a bit of a dent in them from being bashed by the derailleur.

Also, I'm not sure how well the 29er fenders would work with 29x2.35 Big Apples. The 29x2.0 Marathon Supremes I'm using actually measure out a bit under 1.9 inches, and the rear fender clearance is tight. It might work with 2.35s but I wouldn't guarantee it.