S.C.
I'm a runner as well,
all I can say until you hear from your doc is take some motrin for the muscle pain, it's an anit inflammatory it will heal the muscles, also stretch really good after do a 5 min warm up before then stretch before but dont skip that 5 min warm up! you will injure yourself. As for running 3 -4 miles maybe pace yourself slower, though you've been doing it a long time who knows things change, practice expanding you lung capacity deep long breaths. especially when your sick oxygen naturally heals alot of things. good luck!