I have an update. I went to my regular vet yesterday with the cats, and Fleetwood tagged along. I talked to her about everything.
She said that the panosteitis would explain it all. She said that it is, in some form, an auto-immune disease. So I guess his immune system flares every time he has inflammation in his legs... And the skin, behavior, digestive problems, etc can all be attributed to this disease.
She gave me prednisone to use if he has a really bad day, and that should help. She herself is a autoimmune patient, so she could relate!
Does that sound right?