Page 78 of “5/3/1 Second Edition” is basically the information you are looking for. Jim wrote the template for Monday and Wednesday or Thursday, but if the only option is to barbell train on the weekends, you work with what you have, give the 5/3/1 program an honest effort, follow Jim’s principles, and make progress. That is how I’ve been training since mid May because I haven’t had much time during the week and I’m physically too tired and weak after I get home from work to consistently have decent barbell workouts. So far it’s been working well!
Lower and upper days are still split, so excessive spinal loading is not an issue if you have at least a little training experience and you are able to plan assistance exercises accordingly. I’m using the squat, bench, deadlift, and push press for the main lifts. All my lower body sessions begin with power cleans because they warm me up well, I enjoy them, my technique sucks and I need the practice. All upper body days begin with light to moderate behind the neck presses because I tore a rotator cuff 13 years ago and the PBN has probably helped strengthen and stabilize my shoulder better than any other exercise.
Mid week, I usually throw in some rear delt or rotator cuff work and my shoulder feels good as long as I keep up with this. Walking lunges are another important part of my mid week routine. They seem to help keep my lower back happy. And barefoot calf raises help strengthen and reduce discomfort in my feet. I suspect one reason my feet are weak is from wearing boots with a shank for work all week. A lot of my conditioning comes at work: climbing trees, dragging brush, carrying wood, working on steep hills, etc, but I get some running and jumping in when I can. That is what I do and why I do it. Hope that helps!