My son has been having stomach pains and a sore neck (primarily the left side) for 4-5 day's now, he's been pretty miserable and can't get comfortable?

Hummmmm: If he's that uncomfortable he should really been seen by a physician. In the meantime you can try warm moist heat to his neck (heating pad or towel from dryer) and a little acetaminophen for the pain. Given that his stomach is troubling him steer clear of NSAIDs right now - they can be a little hard on the stomach. Encourage fluids. Most importantly, see your pediatrician promptly.