Stanza III Summary

Get out the microscope, because we’re going through this poem line-by-line.

And then I heard them lift a Box
And creak across my Soul

The funeral service is over. How do we know? Because now the mourners have picked up the casket ("Box") so that it can be buried.
Here the environment of the poem moves into spiritual territory, as announced by the word "Soul."
The Soul, apparently, is the floor or ground where the funeral is being held. The word "creak" leads us to think that the Soul must be made of wood – old, creaky wood.

With those same Boots of Lead, again,
Then Space–began to toll,

The mourners who carry the casket seem to be wearing boots made of lead, a very heavy metal.
After they have walked across the speaker's soul, "Space" begins to "toll" like a bell. Church bells often toll at the end of a service, so we're still in religious territory here. She imagines that her mind or soul is like an entire universe containing a vast empty space.
Moreover, why does the speaker say, "those same Boots [...] again" as if she knows them already? She recognizes the boots from some earlier experience.