Also read in this thread:
How to build a basic lifting routine using 5/3/1
A Wendler 5 3 1 Calculator is located here.
531 For Singles is located here.
Novice 531 Fullbody workout
The problem with beginners, is they get to impatient and want to tweak everything right away without letting the program work its course. I only did two months of the squat before entering my a power-lifting meet myself, but I am no beginner.
My max squat before hand was 475lbs which I hadn't done in a long time. I had used 90% of my competition squat which was 455x 90% rounded it to 410, and without lifting any heavier than 465 which was just done 10 days before(not part of wendlers) while testing my 2nd attempts, at the competition I smashed 495(20lb pr)with more in the tank so Wendler's program does definitely work work, and is worth investing time in.
However I did not only do wendler. I inter-graded his program in with my meet prep. For example it looked like this:
I used the plan for my Bench/Strict press & Squat/Deadlift/Front Squat
Wendler Phase 1
W1 5's (5-9reps)
W2 3's (3-5reps)
W3 1's (1-3reps)
W4 De-loaded on the bench and Squat I went for M/E on the strict press
W5 Continued Max Effort Singles for all my lifts
Wendler's Phase 2
W6 5's(got smashed)
W7 3's (recovered)
W8 1's(a little beat up)
W9 DE-LOADED ( I just took the whole week off)
W10 Worked up M/E for all my 2nd attempts in Bench, Squat and 3inch mat pull for deadlift
W11 Worked up to openers
W12 +3 days De-loaded (just rested)
W13 -3 days, 10days later from touching weights, S.F.W! MEET
Now why you may ask, did I not fully follow Wendler's SCARED advices, because I needed to get ready for a meet that tested my one rep maxes, and feel Rep Max Calculators only give you any idea what you CAN lift, until you have actually felt that weight in your hands, it is all just speculation. Now what did I learn from this, give wendler's program 3 months before you go for singles, and de-load on de-load week, at least for Squats and Deads.
I am currently running it over with my Squat, Axle clean and strict press and narrow grip bench and am loving the results right now.
I found my bench press,front squat and deadlift respond better to my own training methods, and since I am getting ready for strongman, bench press sits on the back burner for my overhead press, and deadlifts get substituted for heavy events and deadlift variations.
Now from time to time I may round up or down 5-10lbs if I feel I for my 3rd week I am supposed to get 1-3 reps, and I think with the current weight I will do 5-7, but that is because I train by instinct and listen to my body. Wendler's 5/3/1 in my opinion is the best training program hands down for raw strength, and longevity on the market right now.
However it is just a guideline like everything else. It isn't going to magically put pounds on your lifts, you need to put in hardwork yourself. If you feel it isn't working on a certain lift, switch part of it out, but if it isn't broke don't try and fix it.