hey, I am no expert and cant give specific advice but here is what happened to me.
i started to run three years ago and consequently used muscles in a way i had never used before and so faced knee, back and shoulder pain for almost a couple of months. i kept icing them, bandaging them and going to the local physio for various treatments. Infact I single handedly financially supported the entire physiotherapy department of the local hospital for those two months
slowly things got better, i also did some strength training so the muscles grew stronger over time.
good luck , dont get discouraged, over the length of the training program you will run into several such events besides work commitments etc. a few days rest does not put you so far back as you think
