I ran 5/3/1 while I was recovering from ACL reconstruction and getting my meniscus trimmed out. You can actually follow the entire process, from 2 weeks post op to full recovery, in my log here
But for some quick tips
-For squats, I did single leg squats on a plyo box with the uninjured leg to start with. I did 5x10 unweighted before moving up to using a kettlebell in my freehand before eventually moving onto a safety squat bar on my back. Standing on the plyobox allowed me to have my healing leg locked in a knee brace without having to do a really ridiculous pistol squat.
-Once I had a little more confidence in the knee, I switched to 1 legged SSB box squats, like this
The key was to use the pin to hold onto with the hand of the injured side (my left in this case). This allowed me to have the healing knee extended/out in front of me and use the upperbody to help even out the squat. It was like half a Hatfield squat.
-For "deadlifts", I did seated good mornings. I'd rotate between 3 different types; Seated axle zerchers off pins, seated chain suspended SSB good mornings, and seated chain suspended buffalo bar good mornings. These were videos of my last 3 good morning workouts before I was cleared to train.
I was basically going Max effort on them.
For assistance work, I would do band leg curls and extensions with the good leg. For the healing leg, I would do a ton of flexing and visualization. I have no idea if it helped, but I heard from enough folks that it would, so I figured why not.
For core work, blast strap fallouts (stand on one foot) and reverse hypers went a long way.
Hope that helps.