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|Don't know if you have it, but Jay Winik's book April 1865 goes into some detail about guerrillas after and during the war. I don't remember if he specifically mentions deserters, I think they were just your average raiders, but its interesting information anyway.
I did my thesis on substitutes, it was actually Union subs from Boston who subsituted from July 1863 to September 1863, most of whom fought at Cold Harbor, Mine Run campaign, some at Petersburg. Of course a majority of them deserted, as was the reputation, and I found a little (emphasis on little) info on some of the deserters, most of whom ended up back at home or way far away in a territory.