Rather than answer all the questions I'm going to stick with the main question.
Q. What is the Biblical justification for different denominations?
A. What is the Biblical justification for one Church?
There should never have been different denominations (or branches of belief) but as Paul stated here in Eph 4:1-16. There is only one body of believers, the Church.
3 Endeavouring to keep the unity of the Spirit in the bond of peace.
4 There is one body, and one Spirit, even as ye are called in one hope
of your calling;
5 One Lord, one faith, one baptism,
14 That we henceforth be no more
children, tossed to and fro, and carried about with every wind of
doctrine, by the sleight of men, and cunning craftiness, whereby they
lie in wait to deceive;
15 But speaking the truth in love, may grow up
into him in all things, which is the head, even Christ:
16 From whom
the whole body fitly joined together and compacted by that which every
joint supplieth, according to the effectual working in the measure of
every part, maketh increase of the body unto the edifying of itself in
Paul did grapple with the beginnings of denominations in his day too. It was because the believers brought in traditions and beliefs from the old testament law that they thought were still required, such as circumcision.
Why did it occur? because of many reasons. But you could say simply that it's because the people who have started these denominations haven't believed and followed the one who is to guide us into all truth. So instead they have substituted it with corrupted understanding and taught this corruption to others who do not have the knowledge.
Another reason can be because of poor translating. There are many words added in some translations that are not there in the original text. These words are added to help clarify the text but sometimes they change the meaning. At least the King James writers had the integrity to italicise added words.
Even with poor translation though, the Holy Spirit can still guide you into truth. And the only way to be guided is to walk in the spirit as in Romans 8. We need to study the text and ask the right questions. Did you not know that you can ask the Holy Spirit in you questions about what you're reading? In the end it comes down to a relationship with Jesus. Not everyone in the church has a relationship. This is why Jesus said in Matt 7:21-23 -
21 Not every one that says unto me, Lord, Lord, shall enter into the
kingdom of heaven; but he that does the will of my Father who is in
22 Many will say to me in that day, Lord, Lord, have we not prophesied
in your name? and in your name have cast out demons? and in your name
done many wonderful works?
23 And then will I profess unto them, I never knew you: depart from me,
you that work iniquity.
It's because it's all about the relationship.