I prefer the term painful to negative because I feel negative sets up those black and white categories once again. Painful on the other hand is simply an accurate description of the sensations they create in both body and mind. Yes, emotions certainly affect our physical body and if you have persistent, chronic pain that is not responsive to traditional treatment approaches, it may be wise to consider the pain from a different perspective such as your spiritual, social, or emotional health. You are not crazy, the perception of your pain is very real. It just may take a creative angle to get to the core of it, especially if it didn't arise from a specific acute injury.
Let's look at a few painful emotions and how they might manifest in your physical body and what they might be trying to communicate to you, and then simply ask yourself "What might help?" and stay with yourself until you feel the answer in your gut not just your head.
JEALOUSY: Chronic headaches, likely from the pressure you put on yourself to obtain what you perceive you are lacking and others have. What might help?
FRUSTRATION: A sore shoulder that feels stuck, likely from trying to move in directions that are forced, and doesn't respect the natural flow of what is now. What might help?
GRIEF: A deep ache in your chest, likely the unoccupied space that used to be filled by something or someone no longer present in a concrete, logical sense. What might help?
Emotions do not operate independently so it's more common to have a cocktail of feelings at any given moment, sometimes very conflicting. The trick is to be able to recognize and hold space for each part of your emotional landscape, for example, "I'm disappointed and hopeful". As humans, there is typically so much going on behind the scenes with each of us that is rarely fully communicated to others or even ourselves for that matter. If you can be even 5% more mindful you may find simple awareness serves as a tonic.