I injured my back towards the end of the summer and I had to take about six weeks off from any squatting. I don't think 5/3/1 is the best choice for a situation like this because at this point, your weights should be moving back up at a rate of 10 to 20 lbs a week. Doing 5/3/1 at this point would probably just slow down your progression.
I came back with a higher level of strength than you did, but I basically followed this template and you should be able to do the same:
Squat once a week
1 non-barbell lower body accessory lift
Low back work
Week 1 - 3 X 10
Week 2 - 3 X 8
Week 3/4/5/6/7 - 3 X 6
Week 8/9/10/11/12/13/14/15/16/17 - 4 X 4
Over the first three weeks I added 20-30 lbs a session, but I eventually cut it down to 10 lbs each week. The amount of weight I added was based on how easy I felt I'd gotten the lift. I didn't need a real deload until I'd squatted for about 14 weeks, but feel free to work it in where you feel it's necessary. You can also stick with the 3 X 6 as long as you feel you can, but I would put more importance on adding 10 lbs a week rather than sticking to that rep range. Once you feel you no longer can hit the required reps at that weight, drop the reps down, bump up the sets and keep the same weight.
This is basically progressive overload and I feel like it's very useful in a situation where you're detrained. Hope this was useful.