Any suggestions of textbook titles would be much appreciated. If you can give a reason for why you like that textbook, that would help as well when I go about choosing.
My wife is a new graduate student, and is currently working to get herself up to speed on molecular genetics for her current research. A quick survey of our bedroom floor reveals:
"Fundamentals of Molecular Evolution", 2nd Edition, Dan Graur and Wen-Hsiung Li. 2000, Sinauer Asscts.
"Molecular Evolution: A Phylogenetic Approach", Roderic Page and Edward Holmes. 1998, Blackwell Science.
"Molecular Systematics", 2nd Edition, Hillis, Moritz, and Mable. 1996, Sinauer Asscts.
The last appears to be the most "encyclopedic", it's easily as thick as the two others put together.
Prior to her graduate studies my wife had no particular, in-depth training in molecular genetics, so these should be at about the level you're looking for.
Hopefully this helps. These are the books reccommended to her by the entomology department at the University of Missouri at Columbia, one of the foremost ento programs in the country. Other than that, as a total biology n00b I can't really assess their quality.