I think that
Unlike Guatemala and other countries where we have reports on civil war fatalities and disappearances, we don't really have any statistical analysis of the Salvadoran war. It's not that we don't know anything about the war.
Some other interesting things to come out of the conference were reports that the ERP believed that the truth commission's findings were meant to isolate them and to make them take the fall for all/most FMLN crimes. This contributed to their break from the party a few years later.
There have been several excellent works that touch on the Salvadoran right both by journalists (Raymond Bonner, Mark Danner, Alma Guillermoprieto, Tina Rosenberg) and academics (William Stanley, Elisabeth Wood, Charles Call, Charles Brockett) but it remains an understudied area. However, there seems to have been consensus at the conference that the Salvadoran military hasn't gotten as much attention as it should.
Part of that is because the military, obviously, has an incentive not to talk about its actions during the war - whether that is because of what its forces actually did or because of a fear of future prosecutions. It's also because academics just haven't tackled the issue. There have been a few books about the Salvadoran armed forces and how its doctrine developed but they have been written by US military advisers, not academics.
Just looking quickly at a Wikipedia entry on El Mozote, one reads
The Atlacatl Battalion went on to commit many more atrocities, including, nine years later, the murder of six Jesuit priests and their cook and her daughter in November 1989.I think that we'd like to know more about the history of the Atlacatl and the military between between December 1981 and November 1989.
Likewise, I don't really know of much research carried out on civil-military relations in El Salvador - other than the military didn't answer to Duarte, what was their relationship like? From what I understand, it got worse after the FMLN kidnapped his daughter but it was never very good.
Another thing that came out of the comments on my piece was some criticism of our desire to better understand the US' role in the conflict. We "know" that the "US" supported the "government" but it would be more helpful if we had a more complete understanding of how the US Embassy, State Department, CIA, White House, Congress, other US agencies, Duarte and the PDC, D'Aubuisson and the right, and the Salvadoran military interacted with each other. We have parts of the story in lots of different places but there's no single work that really tries to put it all together.
There's a book on Killing Hope that is very critical of the US government that keeps popping up on Al Jazeera commentary, but it doesn't differentiate among the different US actors and Salvadoran agency is non-existent. It's as if the Salvadoran military and the government played no role in the country's civil war other than acting as "yes" men for the government. I'm sure that some people adhere to this characterization of the US-Salvadoran relationship but I don't.
There's also a tendency to over-rely upon former US Ambassador to El Salvador Robert White's testimony. What he says is very important, and disturbing, but he was out as ambassador in 1981 right at the beginning of the war.
Hopefully, future conferences will focus more on other issues like refugees and internally displaced persons, the psychological and physical wounds from the war, the economic and environmental costs, and the role of the democratic/non-violent left. This was just the first meeting.
Sorry for not putting this together into a more cohesive post but I put it together over the weekend and then just let it sit there for a bit.