I just finished reading Ricardo Saenz de Tejada's Revolucionarios en Tiempos de Paz: Rompimientos y recomposicion en las izquierdas de Guatemala y El Salvador. I purchased the book a few years ago but never made my way entirely through it. I don't have the patience to read 250 pages of Spanish when I am in the states.
Anyway, it's a book that I would highly recommend for those interested in learning more about the FMLN in El Salvador and the URNG in Guatemala. While Saenz de Tejada does discuss the wars, the peace processes, and postwar developments in each country, the emphasis is always on the FMLN and URNG organizations. That emphasis really sets it apart from most of the other works that have been done on the Salvadoran and Guatemalan conflicts.
The book was published in February 2007 which means that it does not cover the FMLN's rebound from its 2006 defeat in presidential elections to its victory in 2009. Less interesting, perhaps, it does not address the URNG's weak electoral performance in elections of late 2007.
There's a lot more to each group's history but this is as good a start (really more than a start) as any.