On newer movies that prove troublesome ripping with DVDShrink, I just go ahead and rip the entire thing as files using the built-in ripper within AnyDVD. Shrink has never shown any bad behavior on those files, once ripped to the hard drive.
I virtually always do movie only backups, so I have never had sufficient reason to learn PGCEdit very well....probably should, but need incentive!
DVDRebuilder Pro has proved to be an excellent program for me as well. Lately I've been using the HC encoder, and haven't seen any reason to use ProCoder. But I back up dvds very infrequently these days anyway. Have moved on to Blu ray for those movies I want badly enough to buy.