Hi DesertRat...well, it sounds to me like your body is telling you to stop the jogging. It may very well tell you the opposite in a couple of days...just listen to it, is all.
I remember reading in the archives posts from 'Pepe'. Pepe ran a whole lot and got faster and faster and felt better and better! So, for some people the exercise is just great. Others feel that their energy saved from not eating, should be directed to any healing they need. (not to say that pepe didn't receive that too!)
Brisk walks are healthful....your body will tell you exactly what it needs.
Maybe someone else can answer your question about muscle/protein stuff!