If I had already done 2 cycle of BBB then I would start at week 8 and go with option 2, but that's highly individual based on focus. Spending more time and going back to week 1 is still an option but that's something if you want to focus on more hypertrophy. If at this point you feel like your 6 weeks of BBB added quality mass and you're ready to work up and hit some PRs then go for it.
I would hold back some days and push on other days. Again kind of individual. I think it's smart to hold back on 5's week to give yourself a break but I know some people are able to and benefit from pushing every week. Try each one out and determine which benefits you more.
As to assistance exercises and the back question in general yeah it's again kind of up to the person designing the program. 5/3/1 is a good template, it can be altered in 1000s of ways to fit different goals. I would only run it hitting back every day if you think that's a big weakpoint for you or if your goal is increased back strength/mass to carry over into the main lifts.
Your best bet as to picking assistance work is to video your lifts, look at where you have sticking points, then picking 1-3 movements that work on hitting this weakness. For me I know that back work is important to all my lifts so I hit it every day. I also know that I have trouble keeping upright squatting as well as shaking on pulls around the knee area which has been fixed before with ab work for me so I hit lots of rollouts and planks on my lower days. For OH I suck at the top so I hit lots of tricep work. Bench, I suck off my chest and hit more wide grip work on backdown sets and dips etc.
I hope that gives some indication of what to do with 5/3/1. There's no real WRONG way to use 5/3/1. There are more intelligent ways that Jim can tell you directly, but in the end it is only a template and you have to use your head and think "what do I need and how do I keep it within the 4 core principles"