Why will Bnei Yisrael and Bnei Yehudah come then?
Radak: When Bavel will be destroyed, Yisrael will leave exile, via Koresh Melech Paras.
Were Yisrael in exile with Yehudah in Bavel? Sancheriv exiled Yisrael earlier, to other places!
Radak: When the 10 tribes were exiled, s small number remained in Eretz [Yisrael] scattered, like it says in the words of Chizkiyah and Yoshiyah. Those few (were exiled to Bavel, and) will return together with Yehudah, via Koresh Melech Paras.
Malbim: Shevet Levi 1 and Binyamin will join with Yehudah.
Why does he omit Shimon? Shimon inherited amidst Yehudah! Even if Shimon was scattered amidst Yisrael (refer to Bereishis 49:7:2:2-3), also Levi was scattered! (PF)
Why will they be crying?
Refer to 31:8:1:1-4 and the note there.