Isaiah 54
5 For thy Maker is thine husband; the LORD of hosts is his name; and thy Redeemer the Holy One of Israel; The God of the whole earth shall he be called.
6 For the LORD hath called thee as a woman forsaken and grieved in spirit, and a wife of youth, when thou wast refused, saith thy God.
7 For a small moment have I forsaken thee; but with great mercies will I gather thee.
8 In a little wrath I hid my face from thee for a moment; but with everlasting kindness will I have mercy on thee, saith the LORD thy Redeemer.
9 For this is as the waters of Noah unto me: for as I have sworn that the waters of Noah should no more go over the earth; so have I sworn that I would not be wroth with thee, nor rebuke thee.
10 For the mountains shall depart, and the hills be removed; but my kindness shall not depart from thee, neither shall the covenant of my peace be removed, saith the LORD that hath mercy on thee.
11 O thou afflicted, tossed with tempest, and not comforted, behold, I will lay thy stones with fair colours, and lay thy foundations with sapphires.
12 And I will make thy windows of agates, and thy gates of carbuncles, and all thy borders of pleasant stones.
I see the same outward application that you describe to the church.
But at the same time, I also see an inward application to the prodigal son (and all like him, i.e. the redeemed of the Lord). The prodigal son was afflicted, grieved in spirit, forsaken for a moment, but gathered back to God in mercy. The prodigal son's mountains departed & hills were removed (i.e. his high places, his idols were destroyed) when the flood of God's judgment passed through him. And when he repented, God laid precious stones within him (Christ).
Israel = redeemed of the Lord, crucified with Christ & raised again
Flood = judgment of God
Those destroyed by flood = the beast, carnal man, destroyed, tares gathered out and burned.
Ark = Christ
Noah & family = the righteous, new man, Christ in you
See Psalm 107.