The office leaves him at noon. Pelosi would get the nod at that point.
Regarding swearing in of Pence it’s a good question. Or rephrasing it, at what point would they decide not to bother? There was a several hour delay from JFK being declared dead to LBJ’s swearing in on the plane back to DC.
But they would go a day or two? I doubt it. What’s the limit? Might depend on what Pence wanted to do, no doubt in consultation with Pelosi and Roberts.
Re Airforce One, it’s a call sign that follows the President, not the equipment. He could take off in AF1 and it would cease being AF1 at noon even if it was still in the air.