I wish I knew more, but with the mention of hives, I can at least pass on one thing to check out: mast cell activation disorder.
This is where the body has problems with the mast cells, which usually trigger with an allergic reaction. In folks with this disorder, the mast cells trigger with things they shouldn't, and can gives hives, pain, and other problems while many of the tests for any other issues are negative.
They can cause headaches and gut issues, too.
Mastocytosis and MCAD are common terms used to refer to these, as they are related conditions. The best information I've found on this, to be looked over quickly, is on a few facebook groups, actually, for MCAD or mastocytosis. There is also a mastocytosis society that you can google for information, although it has less information on MCAD itself.
This is listed as a very rare disorder. However, some experts are speculating that it may be much more common than previously thought, and simply rarely diagnosed, instead. You have to find a doctor knowledgeable in this to test for it, or learn a lot about the tests you need and find a doctor willing to order them.