Verses 5 and 6 return to the theme in 2 Nephi 12:2-5. Isaiah begins with a declaration of building a dwelling place of the Lord, then recounts the judgements that will be necessary before that is to occur. At the end of this conceptual section, Isaiah closes the vision with a repetition of the beginning section. Verses 5 and 6 here reprise the theme of the building of a dwelling place for the Lord.
The "cloud of smoke by day and the shining of a flaming fire by night" is a very clear reference to the experience of Israel with the Lord during their travels in the wilderness: "Ex. 13:21 And the LORD went before them by day in a pillar of a cloud, to lead them the way; and by night in a pillar of fire, to give them light; to go by day and night."
The "glory of Zion" is another reference to the Lord himself. The presence of the Lord is indicated in the cloud and the fire, and his physical presence (also implied by his "glory") will be the defense of Israel. Their God will be their protector, not the hand of man.
In verse 6, the reference to the tabernacle clearly follows from the cloud and the fire in the previous verse. This is the temple of the Lord, and it will be for them a shelter. In verse 6 the specific items mentioned are the natural elements, but those elements stand for all that might cause discomfort. The dwelling place of the Lord is no ordinary house to keep out the rain of the skies, but rather a special place to keep out all of the storms that might rage against the soul.