What is the importance of the order of the chapters in Guns, Germs, and Steel? Why for example, is "Collision at Cajamarca" - which describes events that occur thousands of years after those described in the subsequent chapters- placed where it is?
The order in which Diamond arranges his chapters makes a great deal of sense. In particular, the placement of Chapter 3 (Collision at Cajamarca) is very reasonable. This is because Chapter 3 (along with the previous chapters) sets up the questions that will then be answered in the rest of the book.
Chapter 3 is important because it lays out what Diamond says are the proximate causes of European domination of the world. It tells us all the factors that, in Diamond’s mind, allowed the Spanish to defeat the Incas. It is important to put that chapter before all of the later chapters because we have to understand what the proximate causes of European domination are before we can talk about why they came to be. If Diamond had simply started out explaining why some areas of the world domesticated plants before others, we would be confused. We would not know why that was relevant. By putting Chapter 3 before the other chapters, Diamond lets us understand why we are talking about things like food production.
Overall, the sequence of the parts of the book makes sense. In Part One, he lays out the general questions that he is trying to answer. In Part Two, he explains why food production happened earlier in some places than in others. In Part Three, he explains how food production led to power and wealth. In Part Four, he applies his theory to the various parts of the world. This is a logical sequence in which to write the book.