I did 5/3/1 for about 1.5 years and considering myself as an intermediate lifter.
At the end of summer, I found another program (8 weeks, not from Jim) where they put you to squat 3 times a week. Now I had my issues with regeneration, BUT I did some awesome progress in squat.
I am currently waiting for my knee to be healed after a meniscus-operation (I tore it in spring 2017) and will restart my training with a mass-phase (see another thread in this forum).
After this mass-phase I really want to get back to 5/3/1 (love the simplicity), but I also really want to squat 2 times a week. Can anyone suggest a template where you can squat twice?