Unsurprisingly, only 21 of the 50 pages pertains to the validity of the evolutionary model; the other 29 are extraneous. Since genetics and molecular biology are my areas of interest, I decided to respond to the 13 of the pages that pertain to those areas (as well as some anatomy in the portion on vestiges).
UPDATE (10-19-09): WOTM has radically changed the 50 page intro and will no longer be omitting chapters 9 and 11-13.
The Evolutionary Process (p.20-21)
Evolution's Difficult Questions (p.26-30)
Vestigial Organs-Leftovers Again? (p.30-31)
The old pdf (as of 9-22-09, when I accessed it from the Living Waters site) can be found