Writing PhD thesis as part of consortium project
A thesis is not an academic paper - you are supposed to be a little bit more self-centred than usual to show that you have applied the right kind of thinking to the problem, and the right methods.
Since you have re-done a lot of the analysis yourself because the collaborators did a poor/uninterested job, I would acknowledge the collaborators in the acknowledgements section at the beginning of the thesis, but then stick as much as you can to the work you did and the story that follows from there.

The alternative is that you don't talk about the work you did (bad idea), and might even give the reader the impression that you didn't know better having signed off on a sub-standard analysis (also bad idea).

Also, as someone in a similar situation, can you raise the issue with someone at the consortia? They need to know that PhDs are having a hard time forming a traditional "thesis" of work when they are being dropped into a service role rather than a traditional open-ended PhD, and that funding in the future must go to the labs that have thought about this problem in advance.