For the contents which is based on the collaboration with others (I acknowledged it by referring co-author paper), how to clearly indicate my own contribution (is that necessary )or I can just make it clear in the VIVA on the examiner’s request ?

I tihnk you do need to make it very clear, perhaps in your methodology chapter exactly what you contributed. But just describing that would make no sense without the rest of the context (i.e. other people's work). I'm going through this at the moment, and the best way I found to show it was to do a big flow diagram at the start of the methodology chapter, and highlight the things I did. hen it shows where your work fits in.

We have the same issue. In my case , I have to describe other people's work to keep the thesis intact . But I found it difficult by using a clear nice-looking diagram to do that. They are so interlaced.
I ask this also because I read other PhD thesis in my lab, they actually describe other people's work without well acknowledge. That's supervisor's work, so it seem not really matter(his supervisor don't really care about that).

Another thing is if you adopt other people's code(I am working in EE field). You could spend months to study it, understand it. Finally there is maybe only 10 lines change within a 10000 line original codes to get the code you needed. How to clear define the bound between you and other people's work.