Well, first off US Law does cover foreigners and things that happen on foreign soil in a lot of cases. If you go back to the Supreme Court decision after the civil war it said that it was unconstitutional to use Military Tribunals against civilians in an area where normal courts were operating. So that leaves two clear cases where military tribunals could still be used:
Against foreign military people.
Against civilians in places where normal courts are not operating
These are exactly the conditions that were in place in the War on Terror in Iraq and Afghanistan. The US Military arrested people who they termed "enemy combatants" (thus depriving them of Prisoner of War status, as if they had belonged to a legitimate national Army) and has held them, some for a very long time indeed.
That got challenged (not just the holding, but the trials of them) all the way up to the Supreme Court, lost one round, rules got slightly re-written, and then approved.
So we can keep doing what we are doing at Gitmo, in the same circumstances, no problem.
Now let's go to the idea that at some point in the near future that President Trump is going to unleash the Marines to go arrest 30,000 people which there are sealed warrants for in the USA, take them to Gitmo, and try them in military tribunals.
If we are talking about the people we all know and hate, like Susan Rice, Valerie Jarrett, Bruce Ohr, attorneys at Perkins Coie, up to an including Hillary and Huma -- this would clearly violate the case law around using military tribunals because A) they are not members of a foreign military and B) the civil courts in America are functioning.
I do not believe President Trump would ever order something that would clearly be unconstitutional, and almost certainly result in a humiliating defeat in the Supreme Court upon review (which would happen instantly, like Bush V. Gore).
You said: So tossing all the Lincoln stuff aside, what in your mind is the appropriate method, law and court that all of these people working AGAINST our government should be
Ooops, sorry for going over the Lincoln stuff.
I think that the Jeff Sessions plan of arresting them one or two at a time and trying them in Federal Courts, as you say, outside if the District (or NYC, or 9th District) would be the way to go.
So the Huber move, if it's ever acted on, would be brilliant. As you say, not in D.C.
Guess what State is way-out-west, votes solidly Republican, and *not* in the 9th district?
If you said "UTAH" you are a winner!