As a place to start, can you follow up with your doctor and ask for a more detailed explanation of the results? Or would you want to get a second opinion?

From what you mentioned, it sounds like the letter they sent is contradictory to the pathology report.

If the colonoscopy and endoscopy really do show nothing significant, then you could talk to them about options for managing your symptoms. Now, I know from experience that conversation might not yield much, but I feel it would be ideal to rule out the other things before moving on to figuring out other ways that might give you more relief.