I don't understand the problem. But I do understand the desire to keep the json definition simple and concise.

If you need additional fields in the json to hold comments, why not add the fields however you want? And if you need meta-data for the parser, you could add it the same way. In a project, i am working on right now, we simply use a attribute called "comment", for comments.

e.g. use "_" as a prefix to mark comments, and then tell you applications to ignore these attributes.

    {
    "mystring": "string123",
    "_mystring": "i am a comment for mystring",
    "mynum": 123,
    "_mynum": "i am a comment for mynum",
    "comment": "i am a comment for the entire object"
    }