I did have the experience of having aches and pains increase as I progressed further into the program. In fact, when I finished, I took a week off from running entirely to give myself some rest.  I'm in my mid40s, so my body needed some time to adjust to the activity!

I'm not sure I can help much to figure out the pain other than to say that if it's pain rather than discomfort, that may be a sign to take a break.

The side stitch may be caused by shallow breathing.

In terms of the muscle soreness/discomfort, try incorporating some yoga on off days and/or use a foam roller -- I find that the roller in particular really helps me with muscle soreness.  I have one that is 3 feet long, 6 inches in diameter. I use it several times a week on quads, hamstrings, IT band, calves, etc. In particular, I found that I had some really deep muscle soreness in my calves that was causing some pain in my Achilles tendon/PF.

I hope this helps!