First of all, let me congratulate you on your phenomenal success in losing weight and beginning to exercise. This is a really tremendous accomplishment, one which will greatly increase your chances for living a long and healthy life.
Based on your description of the pain you are experiencing, this is likely what is known as a side stitch. These are common pains associated with exercise and they probably indicate that you are pushing yourself too far or too fast. Since your overall goal is to develop healthy and sustainable exercise habits that will serve you for your entire life, I would recommend that you slow down the pace of your training and exercise a bit until you no longer have these pains.
Similarly the pains in your stomach that you have at rest could be related to overexertion and over training - fatigue or strain of the abdominal muscles. On the other hand, pain in the abdomen with eating could be related to a different medical problem altogether. If these pains continue after you slow down your training schedule, or if they are associated with nausea, blood in the stool, or if the pain becomes severe then I would suggest talking to your primary care doctor