Here's my favorite explanation on how the brain interprets pain...
Pain is your body’s natural alarm system. But it’s not always correlated with how much damage has been done. Quite the contrary, actually. Here is a great explanation of how pain is interpreted by the brain.
video credit: Ted Education
Here's my favorite experiment that proves pain is an output of the brain
These guys were brought on Ellen to conduct my favorite pain experiment. If pain was always related to physical damage, how would you explain this?
video credit: The Ellen Degeneres Show (I do not own this video)