1. AWF Edwards has written quite a bit on the Fundamental Theorem of Natural Selection and other related stuff. In 1977 he published a small monograph on the deterministic theory which includes a discussion of the difference between average effect and average effect:

Edwards AWF
Foundations of Mathematical Genetics
Cambridge University Press, 1977.

The monograph also contains the parabolas discussed in Ewens book, and a more recent version of this is also in

Edwards AWF
The Fundamental Theorem of Natural Selection
THEORETICAL POPULATION BIOLOGY 61 (3): 335-337 MAY 2002

2. Here is the ref to Ewens' first population genetics monograph:

Ewens, WJ. Population Genetics. Methuen, 1969

It contained much more detail on the moments of the equilibrium distribution under 2-way mutation and drift, which we read on P.97 (equations (3.25) and (3.26)) of the current book.
There is also a small chapter using elementary branching process theory.

3. Here is the ref to the Shiryayev text:

Shirayev, AN. Probability. Springer-Verlag, 1984

This is a very good basic non-measure-theoretic probability text book-- actually he does talk about a bit of measure theory, but it is not essential. There is not so much on probability generating functions as I thought -- I'll try to find a better reference for that.

4. Various Watterson papers distributed by Grace.

5. Kelly book for reversability -- Chapter 7 for Moran model results.