I was thinking that the time period should be a little earlier than the Jacobite period, concentrating more on clan feuds than royal politics. Electricscotland has a fairly large history section online, a portion of which chronicles some of the clan feuds that went on between 1454 and 1623. It's not all-encompassing, of course, since these things were pretty common and all that, but it's a good start, I thought.

The link: General History of the Highlands

It's the second section.