1)
Why does it say that the honor went from over the Keruv to the threshold?
1.
Rashi: This is the [first stage of] the Shechinah's departure mentioned above (9:3).
2.
Malbim: What will happen now is not in the Keruv's power, only with Hashem's power and Hashgachah. He will command to burn the Heichal, as if He Himself destroys His house, to finish His anger on it and lighten Yisrael's punishment.
2)
Why did the Bayis fill the cloud?
1.
Malbim: The honor traveled to the Bayis like one who goes from Kodesh ha'Kodoshim to outside.
3)
Why was the Chatzer filled with "Nogah Kevod Hashem"?
1.
Radak (3): The honor left via the Chatzer.
