1)
Why does it say "Bone Yerushalayim Hashem"?
1.
Malbim: He Himself builds it via Hashgachah Pratis, to make it "Ir ha'Elokim Kedosh Mishkanei Elyon" (46:5).
2)
Why does it say "Nidchei Yisrael Yechanes"?
1.
Radak: He will enter them to their land.
2.
Malbim #1: Jews cast off to the four corners of the world, He Himself will enter them to Yerushalayim.
3.
Malbim #2: The Shevatim will enter Yerushalayim and be united in it - "k'Ir she'Chubrah Lah Yachdav" (refer to 122:4:1:3).