Kevin,

Not quite sure what specifically you're interested, but here are a few ideas (I will caveat it by saying that information in English on terrorism and conflict in Indonesia is fairly disaggregated compared with that of most other conflict countries):

- The first go-to source is the International Crisis Group. They are viewed as one of the leading experts in Indonesia on conflict and terrorism.
- Nationalism and Ethnic Conflict by Jacques Bertrand
- The Second Front by Kevin Conboy - provides an interesting overview of the history of political Islam in Indonesia
- Political Islam and Violence in Indonesia by Zach Abuza - details the different groups and their relationship in the many small wars in Indonesia (Abuza's interpretation differs somewhat from Sidney Jones at the ICG and others here)
- Reformasi by Kevin O'Rourke - good overview of politics in Indonesia post-Soeharto

Keep in mind when you are reading all of these that interpretations of the relationship between "small wars" and the larger war (as Kilcullen conceives it) differs greatly among experts in Indonesia and outside.

Hope this helps!