Yeah, in this case it sounds more like a repetitive motion injury (as opposed to have lifted a heavy object, and now it hurts).
Given a tempo avg of 100bpm, and flatpickin' is 2x that for the right hand picking motion, and maybe 3x that for the left hand finger motion... for 8 hours a day? That's alot of tendon tweaks!
[I was gonna say: "Dat's a'spice-ee saus-seeeeeg'e!"]
Maybe consider switching to an electric for these marathons, and see if the pain subsides.