If a prisoner is a civilian, and is taken in the war zone, and is a citizen there, they are entitled to GC4 protections.

100% correct. Not disagreeing, but the only question I would have is what exactly defines a war zone and the battlefield these days?

If they are a combatant, to GC3 protections.

If they are a legal combatant as defined by GCIII (and not Protocol 1 to which we are not a party ;) ), then yes. Otherwise, they could only get GCIV protections.

Exactly what protections are to be determined by an Article 5 hearing. Before that hearing is held, or if it is not held, they are afforded treatment due to either civilians or to prisoners of war.

Yes. I think if there is any question about their status, then they have to be given POW treatment until their status is determined by a proper hearing.

A prisoner taken not on the battlefield, not in the war zone, not fighting, is not a GC issue.

Exactly my point! Pointing to the GCs as governing law for a lot of the people we have in captivity is simply sloppy thinking.

As of today, we are not in armed conflict with any HCPs of which I am aware, so the GCs are largely moot moving forward. We may still be considered an occupying power in Iraq by the GCs, but a SOFA will soon be set up there and I think we already have one with Afghanistan. Furthermore, GC CA3 may still apply to Iraq and Afghanistan because we are essentially helping those countries with their own internal strife, which is what I believe CA3 was meant to cover.

You also left out a couple of other categories. If they were taken in a war zone, fighting or not, but they are not a national of a HCP with which we are in conflict and their home country has regular diplomatic relations with us, then they explicitly do not get any protection from the GCs. Even CA3 wouldn't apply because our conflict with the HCP is of an international character. Their captivity would be purely a diplomatic issue between us and their home country and other international law would govern how they must be treated. Their captivity need not end when our conflict with the HCP ends either.

So, when we invaded Afghanistan, if we captured a bunch of Pakistani citizens fighting with the Taliban in Afghanistan, then their captivity would be purely a diplomatic issue between us and Pakistan. Their treatment would be governed by other international law (I'm not sure which ones). If we picked up a bunch of Saudis in international waters, whether they fired on us or not, then that would be completely a diplomatic issue between the US and SA and the GCs would not apply at all.

Such a prisoner has to be charged with a crime, they have to be extradited, and they cannot be held under GC for the "duration of conflict".

I agree that the GC "duration of conflict" stuff certainly doesn't apply to such captives. On the other points, while I think you are generally correct, I can certainly think of exceptions. For example, what if there is no extradition treaty in place but the national's govt. explicitly agrees to let you capture them or simply turns them over to you?

If the U.S. wants to conjure a circumstance where he is a war prisoner ...

Yes, I agree that trying to classify such a person a war prisoner under the GCs is extremely muddied thinking. Al-Qaida is not a HCP so the GCs do not apply to our conflict with them. Even if al-Qaida were a HCP somehow, then the only possible way it could apply would be if you could correctly say that the battlefield was everywhere (or at least where they were). But if you did all that, then like you said, you would need to put them into one of the categories that the GCs cover, or at the very least CA3 would apply.

I get fairly upset when I think of KSM, because he was talking before the torture to FBI agents, and a squeaky clean case could have been built and brought against him with an iron clad conviction.

Yes, I think very few convictions, outside of kangaroo courts, will ever come now simply due to our treatment of them.