Hi David,
I’m sorry no one has responded to your question. As far as a book on prefixes and suffixes is concerned, I’m sure some one has written one, but it would probably require some research to find it. In lieu of a book, this might be of some help: http://dcc.dickinson.edu/grammar/latin/formation-words
This is the section on word formation in Allen & Greenough’s Grammar and will give you some information on common suffixes. Many if not most Latin and Greek compound verbs are formed by prefixing a preposition with the verb, so you can also check the section on prepositions: http://dcc.dickinson.edu/grammar/latin/derivation-prepositions
Hopefully, someone with broader experience will be able to point you to something more specific to your needs.
Latin Synonyms (Douthat, 1907) can give an idea of prefixes and how they derive the meaning of the words, but it’s not a specialized treatise dedicated to morphology.