Then, in January 1799, Congress passed the Logan Act, in honor of the volunteer diplomacy of the Philadelphia Quaker, Dr. George Logan, who had gone to France during the preceding year to offer his good influences. He had had interviews with [the French foreign minister] Talleyrand the [five-man executive called the] Directory and was acclaimed a "messenger of peace." [American Secretary of State] Pickering was furious at this interference. The act stated that any individual citizen who represented his country without consent of the department of state was liable to a fine of $5,000 or imprisonment for one year, or both.
The author dismissed the very idea that anyone could or should be prosecuted under the act, and that nobody had been. That is still true decades later.
I don't think the Logan Act could be applied in a first-ever conviction on John Kerry because who believes he represents the American government? Nobody could possibly think that.
And while members of an incoming administration could technically be charged with a violation of the Logan Act for reaching out to foreign leaders to get ready for a new administration, how is that even credible? Are you saying that it is proper for the State Department to block such contact by refusing to grant permission?
Even aside from Congress repealing the act, I imagine the entire issue could be set aside with a blanket State Department policy of granting of consent to members of the incoming administration to talk to represent his country in the name of the soon-to-be new administration. The president-elect would simply supply the State Department of a list of people as they are appointed and the department would rapidly give consent.
Certainly, why have a three-month transition period in presidential administrations if you don't allow a transition over that period (even if it is shorter due to a lack of a clear win in the election that requires further actions)? In the past the transition time would likely make the Logan Act moot because of the travel time to move between North America and Europe, or anywhere else in the world.
But if Kerry is advising Iran on how to cope with the sanctions until a more "flexible" Democrat is president, should Kerry register as a foreign agent? And if he isn't, what then?
Funny enough, Pickering himself was charged with violating the Logan Act, although in the end Congress merely censured him for certain acts related to his freelance diplomacy.