MacCoinnich, A. (2002) "His spirit was given only to warre": conflict and identity in the Scottish Gàidhealtachd, c. 1580- c. 1630.

In: Murdoch, S. and Mackillop, A. (eds.) Fighting for Identity: Scottish Military Experience, c. 1550-1900. Brill, Boston, pp. 133-162. ISBN 9789004128231

This paper provides a glimpse into issues which motivated clans to fight against each other, and either for or against the central government. I am not qualified to comment on it conclusions but it appears well cited.

http://eprints.gla.ac.uk/6908/1/6908.pdf