Better nutrition and hydration before and after a workout. As you run, most of your body is focused on the muscles that are being used and are in immediate need of fuel, and this does not include the stomach. The blood flow to your stomach and digestive system is reduced to a low level, and digestion of food/fuel is slowed a lot. The types and amounts of your consumption of food and liquid before and after your run, will allow you to understand why your stomach hurts and how to eliminate the problem.
The act of running produces a good amount of impact on foot strike. The up and down shaking of the stomach can produce a feeling in the stomach and possible cramping. This may take time for a runner to get used to but can be helped if you take some precautions about what you drink and eat prior to and after each run.
"Exercise physiologist Kitty Consolo, PhD, is cited in Valente's article as suggesting that changes in your diet before a run may need to be made. Avoid heavier, greasier foods and especially dairy and high fiber foods. If you do consume these types of food, make sure to do so many hours ahead of your run (allow up to 24 hours). This will allow ample time for digestion, so food is not sitting undigested in a stomach that's being jostled during your run".
As for liquids, make sure to drink plenty of water at least an hour before your run. Not only can your main running muscles cramp from lack of hydration, but so can your stomach.
Runners, especially beginners, may find that their stomach pain after a run will diminish and even disappear as their fitness level increases. In their clinical study "Gastrointestinal Problems In Distance Running," in the International SportMed Journal, Dr. Stephen M. Simons and Dr. Gregory G Shaskan report that the greater the fitness level of the runner, the fewer the gastrointestinal tract problems. In other words, your G.I. tract gets used to the lessened blood flow for digestion as you run more. The stomach starts to understand how to function more effectively in this state, causing less stomach aches.
The stomach pain after your run, look to the proper nutrition for recovery. Use a recovery drink that combines the right ratio of protein and carbs. that will help your insulin response and the replenishment of glycogen or fuel to your muscles and stomach. Dr. Edmund Burke's book "Optimal Muscle Recovery" recommends a ratio of 4:1 carbohydrates to protein for post-run stomach and muscle recovery. If too much protein is used, it can slow the rate of transfer from the stomach into the bloodstream and delay re-hydration, meaning slower recovery from cramping.
As for the chest pain it could be muscle strain.
But I suggest seeing your doctor to be sure!!
As for knees, do you have GOOD running shoes?
after a run ice your knees elevate them and take