1)
Why does Hashem instruct Moshe to place the lid of the Aron in the Kodesh Kodshim, when in fact, he did so before bringing the Aron into the Kodesh Kodshim (See Pikudei, Sh'mos 40:20-21)?
1.
Ramban: Here too, these are not current instructions; Hashem is merely informing Moshe that the lid of the Aron, together with the Keruvim, were to be located in the Kodesh Kodshim (as well as the Aron itself).