Same as Alpaca - def sports physio, worth their weight in gold. Knee thing sounds very familiar and I was recommended exercises and off-the-shelf orthotics. Check out your local running club to see who they use.
I went to see a podiatrist and was given orthotics. I have mild hypermobility which was causing me to repeatedly put at strain on certain parts of the foot, the orthotics are enough to mean I can do short runs.
My shoulder pain turned out to be frozen shoulder. There are some gentle exercises to try but not a great deal that can be done about it; it eases off eventually. If in doubt a physio might help. I've been getting some sports massage and that helped loosen the shoulders enormously.
A physio with an interest in sports, one who does acupuncture ideally. My private physio is ace as she'll beat my back into shape, mobilise the manky bits, put needles into the inflamed bits and give me exercises to sort it all out in the long term. She also ordered very reasonable orthotics which she was able to adjust with the supplied bits to support my feet until they were stronger from the exercises.
She's def interested in getting you properly better and not coming back again, unlike some practioners I've heard of