I definitely appreciate the death by ones and twos nature of this as being the majority, as well as the primarily unknown who never reached their destinations. And in reading your books there are many times that the fate of folks is not known.

My impression is that total guerrilla warfare losses would be the best overall measure, rather than just trying to account for casualties inflicted by known guerrillas or on known guerrillas. That would include Jayhawker depredations as well as excesses by the militia and other Federal forces. Obviously, many different categories result so the tabulation is complex. Some were killed by aforementioned types, but others were dispatched by recruiting commands or other regulars during raids. One person's civilian was another's parole violator, notorious bushwhacker/militia. Obviously a great many soldiers were killed in guerrilla warfare as well. About the only thing I would exclude would be "regular" engagements where substantial forces were involved in more or less regular warfare even if it included various guerrillas, e.g. 1st Battle of Independence. (On the other hand I would chalk up known murders of prisoners by guerrillas during/after the battle as casualties of the guerrilla war. Same could apply to Federal executions for irregular warfare.)

I wouldn't be inclined to include disease/starvation in civilian settings or military death due to non-combat related disease, although the matter is perhaps blurrier with regard to prisoners. If one was imprisoned for abetting guerrillas, then if they died in prison I would attribute their death to the guerrilla war. The jail collapse victims would qualify as casualties of the guerrilla warfare by my reckoning, although their deaths were unintentional.

If anyone has a shot at setting the lower bound for the losses, you appear to be that person, and that is why I raise the subject. A lower bound would at least be a starting point. It would certainly be a thought provoking analysis to make later if it is outside the scope of the present work.