While I love Wendler's approach to the 5/3/1 in regards to the triumvirate (ie. picking only two exercises to pair with the main compound), I feel for the majority of trainees, including myself, there should be a more balanced approach. Jim tends to prefer more of a "split mentality" with his templates, meaning after deadlifting he attacks hammies, and squatting he attacks quads. Predominantly, he loves limiting himself to strictly an upper one day, lower the other. In my opinion, that's absolutely perfect for him since I'm assuming he takes forever with his squat/deadlifting warmups. Additionally, his protein synthesis will be elevated through most of the week since he admitted more than once he's on a good amount of gear throughout the year.
Working with ironaddict for well over a year, I've adopted a lot of his approaches and techniques that have proved to work extremely well. One of which is my personal favorite - Working more of a "whole body" approach. On deadlifting and squatting days, my best successes stemmed from getting my back and biceps finished up before tackling my legs. Why? Well, that's a DC type of mentality. A mental mindgame that allows you to really hammer out "as many as possible" on that final set because after that, you can go riding off into the sunset (or puke and die a slow death). I'm an optimist. :)
I'll only go over the lower days because I think the upper is pretty easy to figure out. I'll advise you to do a shoulder press/isolation at the end of your upper days vs. a back exercise.
WARM-UPS - The biggest, most important part of ANY training program. Not only does it physically and mentally prepare you, but it strengthens your weaknesses. I know some of you have followed my warmup routine in my journal and how important it is. This does NOT count towards the total time in the gym. Your goal is to work on decreasing time between sets, not the amount of weight you use. Keep in mind that in the military, they can do bodyweight exercises many times a day, every day and recover just fine. So how do you know if your out of shape? Well, if your warmups affect your workout, then you're out of shape.
Without going in great detail in exercise selection, this is what I prefer:
Lower back/hammie exercise - Usually the gluteham/hyper combo or pullthroughs
Chest/triceps - Closegrip pushups or bodyweight dips
Lats - Pullups or sometimes grabbing a band and doing some rows
Abs - Leg raises or situps
Reps - Anywhere from 6-15 reps is appropriate.
Time - Either do one exercise at a time, or run a circuit which is what I prefer. Your goal is to work your way down to 30 seconds between sets.
Sets - Start with one set per exercise. Then as your GPP progresses, add another, then another for a total of three sets. Once you get to that point, you may start either increasing the rep range, or very slowing start introducing weight.
One more thing. Sometimes, the exercises I use for the warmups are dictated by the day I'm about to have in the gym. For something like squats/goodmornings day, I much prefer to pull a light 45 lb sled for 5 minutes non-stop. For upper days, I'll get on the stair master for 5 minutes, THEN start my warmups.
Back Width - Really vary this.. My rule of thumb is the lower the rep range, the shorter the rest. Right now I'm doing a 10 sets of 3 w/ 90 seconds rest using my 5 RM. Again, do NOT have a set in stone plan! If you feel like shit, just do 3-4 sets of AMAP (as many as possible). Or do some pulldowns (close/wide/reverse).
Biceps - I personally don't care for curls, but go right ahead. I like forearm exercises like reverse curls, hammer curls, and/or zottman curls for 2-4 sets of 8-12 reps.
Deadlift - 5/3/1 standard template. Do yourself a favor and pause on the floor between reps.
Quads - You name it, just make sure it's low volume. I usually do 2 x 10 leg pressing because it's easier to lay down and press after deadlifting. Another one I usually do is to do backwards sled pulling for 2-4 trips.
Abs - Heavy. These are more important than quads, so if you feel trashed after deadlifting, jump straight to abs.
Back Thickness - Again, vary what you do so long as it doesn't affect the main reason for hitting the gym (squats). In the past I've done barbell rows from the floor upwards of 315 for a 5x5, but I was able to do squats afterwards because it was planned progressions (meaning I never ventured too close to a 5 RM), and built my work capacity for it. SO, I'd recommend chest supported rowing, db rows, cable rows, ect. I'm pretty partial to 5-6 sets of 6 w/ 60-90 seconds between sets heavy. Or if more hypertrophy is your goal, backoff and do 4-5 x 10. Get away from the "3 sets" mentality because you're only working out 3 days a week.
Biceps - After heavy rowing, it more than takes care of your biceps. But if you find yourself waiting for the squat rack, it wouldn't hurt to bust out a few high rep sets.
Squat - 5/3/1 standard template.
Hamstrings - Gluteham raises whenever possible! Pullthroughs, glute/hyper combo, sled dragging, all the way down to banded leg curls. Volume doesn't matter too much depending on your level of preparedness. Yesterday I just did gluteham's for two sets of AMAP (as many as possible).
Abs - Same as above.
DISCLAIMER: I'm keeping my writings here because the second I post something like this in a big public forum, I'll get a full pm box and see a bunch of journals with cable crossovers.