Since my area of research in the history of astronomy will be rather distant from most CFA graduate students, I will not expect them to have read up for our meeting. However, I can offer the following annotated bibliography, among which they may pick and choose:
For examples of the unusual style of Kepler's (Astronomia nova), read the Introduction; the introduction to the Summaries of the Individual Chapters (pp. 78-79 of Donahue's translation); and Chapter 7, "The circumstances under which I happened upon the theory of Mars." The first page of Chapter 45 (p. 455 and the top of 456 in Donahue's translation) is also charming. Students may pick up copies of these materials from Prof. Gingerich.
For the classic "sleepwalking" account of Kepler's work, see Arthur Koestler, The Sleepwalkers, esp. Part 4, Chapter 6, "The Giving of the Laws."
A very good introduction to Kepler's methodology is E.J. Aiton, "Johannes Kepler and the Astronomy without Hypotheses." Japanese Studies in the History of Science, 14 (1975): 49-71.
A more comprehensive account is Bruce Stephenson's excellent book Kepler's Physical Astronomy (1987; paperback ed., Princeton Univ. Press, 1994), esp. Chapter 3, "Astronomia nova."
Finally, for understanding the context of mathematical versus physical astronomy in the sixteenth century, see Robert Westman, "The Melanchthon Circle, Rheticus and the Wittenberg Interpretation of the Copernican Theory." Isis, 66 (1975): 165-193.