It is proper to address Mr. John Doe PhD as Dr. John Doe. You might also address Mr. John Doe PhD as Mr. Doe or Doctor Doe, depending on which reference he prefers.
That's fine, or The John Doe Family.
Master John Doe
The name followed by Jr For example: John Doe Jr
The proper way to address that letter would be "Mr. and Mrs. John Doe."
Mr John Doe and family
Etiquette has come to be more casual in society and you could write John Jr. & Mary Doe, but the proper way is Mr. & Mrs. John Jr.
John Doe, III is an example.
Either: John Doe Smith Or: John Michael Doe
Either: John Doe Smith Or: John Michael Doe
It would be Doctor and Mrs John Doe in most situations. If she was the Doctor it could be Mr and Doctor John Doe, but that is a bit presumptuous to use his name with her title.
The honorific would be The Honorable Councilman/woman John /Jane Doe, and the salutation is Dear Councilman/woman Doe.