1. Is addressed somewhere else in the forum here, in short you can change them gradually, or add the extra to your 1rm in one go.
2. If you get good results it might be worth doing the same program again, if you get no results or regress and you are gaining bodyweight still you might want to try a harder program.
3. Yes, it peaks your training cycle, you should follow the whole program through each block.
4. You can go straight to another program, personally I tend to take a break and try something else for a mental rest, but in hindsight this is usually making me weaker.
5. Just do it at the end of each training session, if it interferes with the program, dial it back.
6. You can modify the program as you see fit, Boris encourages it as you are a co-author he says.
I think if it's your first run then do the program as is, see what works, switch out what doesn't.