I know P-51's from Iwo could reach Japan and shot down many planes covering the B-29s. The zero would have had one hell of a time reaching that altitude. But the Ki-84 and N1K would have had much less of a problem. Did the Japanese air force have the strength to repel any bombers at that point? Also I know they had 2 B-29s flying with them equipped with sensors and equipment to figure out the power and destruction of the bomb, did they have turrets at all?
They did have a tail turret. Just no other armament. This is often obscured in writing about these bombers, but is pretty clear in the official literature (e.g. the Manhattan District History).
As for escort fighters, it would have attracted attention. They were going for what we would today call "security by obscurity" — make it impossible to tell which B-29s had atomic bombs on them, and you make it impossible for the enemy to try and shoot any of them down. The Japanese air force was greatly diminished at that point in the war, and they could only focus their efforts at very promising targets. There were enough B-29s over Japan doing reconnaissance at any one time that most had to be ignored.
The crew of the second bomb were much more worried about fighter resistance, on account of the fact that lone B-29s would now be a target, after Hiroshima. But they did not encounter any fighters. (They did have some very minor AA flak on the Kokura run, but this did not worry them very much, because B-29s can fly very high and are hard to shoot down.)
None of the planes on those missions had significant armament — they were all "Silverplate" bombers, capable of carrying atomic bombs. They did this to have much better flight specifications than a standard B-29. These groups had also all trained with each other for many months, so changing planes or having new crews on other escort planes would create a lot of difficulty.
