Thanks for the pic. I think his problem is (at least in part) that he feels he has nowhere to hide. Get him some much larger rocks/slate pieces or boulders that he can hide behind or between and I suspect that will calm him down
JD's inhabit sluggish waters with dense vegetation in the wild. Plants aren't really an option in captivity as he'll dig them up, but you can give him a more shaded environment and a feeling of security by adding floating plants on the water surface - salvinia, water lettuce, frogbit and so on. They aren't a black water species so black water extract isn't a good idea as it will acidify the water which would be bad for him. JD's are from more alkaline conditions in Central America.