“place of my throne.” The Millennial Temple will not have an ark of the covenant (see commentary on Jeremiah 3:16). Furthermore, Jerusalem itself will be the throne of God (Jer. 3:17).
“the dead bodies of their kings at their shrines.” This enigmatic line is irony, and the “dead bodies of their kings” are the destroyed idols who the people worshiped and obeyed more than Yahweh. They made idols at the high places and treated them like their kings, but those “kings” will be destroyed and be just the broken bodies of statues of idols (cp. Keil and Delitzsch; Commentary on the Old Testament). There are scholars who think that the kings of Judah were buried close enough to the Temple to defile it, but there is no evidence that that ever happened. Even more evidence that the “dead bodies” are the “bodies” (statues) of idol gods is that Ezekiel 43:9 says the Israelites need to put “the dead bodies of their kings” far away from God if He is going to dwell in Jerusalem, but there is no requirement in the law that the dead bodies of ungodly people need to be moved away in order to get God’s blessing. But in contrast, the bodies of the lifeless idols did need to be removed and destroyed.
The Hebrew word translated “shrines” is bamot, which referred to a place that was leveled and built up and on which were placed various idols and objects of worship. Many of the towns had such shrines (see commentary on Num. 33:52).