Respected user , Hi
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I have evaluated your query thoroughly .
* Stomach pain with loose bowels are in relation with intestine infection .
* Recommendations for the same 
  -  Allow plenty of liquids .
  -  Soft , light diet at regular intervals with fresh curd preferable .
  -  Avoid all junk food , bakery items .
  -  Check he chews food thoroughly .
  -  
Drotaverine syrup , zinc suspension , 
metronidazole antibiotic help .
*  Penile pain is separate issue which may be 
phimosis or other issue .
    Need clinical examination .
Hope this clears your query .
Welcome for further guidance .
Regards .