Originally Posted by
yorick
I'm currently doing 5/3/1, and you are correct, Wendler does say he has used the program for beginners and everyone else. The program you choose has a lot to do with diet, rest, recovery, etc. Whether or not you have exhausted linear gains, and if you don't mind the slower progress of 5/3/1, it's not going to kill you, or make you weaker in the long run. It'll just take you longer to get to a point you might have gotten quickly with SS and GOMAD, or even Texas Method.
Another thing to consider is that SS allows lots of practice with the squat. If you are only squatting once a week and haven't really built a good foundation for the movement, I could see form and technique going to shit for some people.
About your original questions: Try to follow the 5/3/1 book to a T if you stay with the program. Leave a rep in the tank on that third all-out set, etc. Try to make sure you get at least the minimum reps on that third set.
Are you having problems getting the proscribed reps in that third week? If so, you might want to back off the volume on your third sets in the other weeks. Like Wendler said, sometimes it's best to just get the proscribed reps in the third set and call it good. You don't have to go balls-to-the wall.