I am not a doctor.
Cramps in your side are probably caused by eating too close to the time you run. Running right after having caffeine might also aggravate the problem, but not necessarily. Also running near the time you are going to have a bowel movement (if you are regular) might increase your chances of a side stitch. For whatever reason your digestive system probably is not slowing down while you are being active.
As for other muscle cramps the most obvious is potassium, easy to test, very cheap blood test, but highly unlikely that is your problem unless you are also anorexic, or have a very poor diet, or have some other medical condition that tends to have low potassium associated with it. More likely you might be vitamin D dificient, especially if you protect yourself from the sun, blood test can confirm it, and if yiu are a woman checking your iron is important, as it carries the oxygen to the muscles. Lastly, if you have other symptoms that might indicate hypothyroid that can lead to muscle weakness and pain. That also is a simple blood test, the basic one is very cheap, and I personally think women should be checked every where for all the things I named attheir yearly check up. Oh, and to add one more, many women I know are borderline low for B12 without supplementation, which affects the nervous system. I never recommend just popping a bunch of megadoses of vitamins until you have an idea of where you really stand by getting the tests done. I have to take huge doses of vitamin D to stay up in the nornal range, I never would have known without the tests. Same with iron.
So to simplify:
BMP (that will include the Potassium)
TSH (that’s the thyroid)
Vitamin D
Vitamin B12
Iron or CBC (depending on what your dctor prefers or both.)
All that might total $100—$200 out of pocket without insurance, but most likely it will be covered by your insurance if you have insurance. Also, it is likely your doctor automatically does at least some of them, and you can see some of it on your last blood test. Special note: if you TSH is >4 it is likely still considered nornal by the lab and GP’s, but endocrinologists would find it worrisome, and worth monitoring more closely.
Last, but not least, remember to stretch after exrecising, not bouncing, just holding stretches for several seconds, to lengthen your muscles and avoid soreness.
Edit: if you are young, in your teens, they might be associated with growing pains.