Choosing Writing Samples for Ph.D application
I'd suggest not to submit a whole thesis. Imagine the frantic look the admission committee members would have when they found out they just printed hundreds of pages.

Ultimately, they care if you can publish. So, definitely keep a and b, and focus on them heavily. For c, I'd suggest do a bit of curating and pick the most interesting chapter that does not overlap with a and b in contents. If none, then I'd suggest the literature review chapter. It's a good section to show your understanding of the field and your skill of information synthesis. 

As for d, they only ask for three; course work (in my opinion) is not worth breaking the quota for. I'd, however, consider submitting if i) it features an extremely innovative idea which may become one of your study objectives, or ii) it acts as the foundation of your then Master's work and publication. It would show that you have the ability to carry and idea forward to fruition, and that's always a plus.

Good luck with the application!