In all 3 cases you have to:
For workflows, use WorkflowManager and its methods getWorkflowClone(name) and updateWorkflowNameAndDescription(username, workflow, newName, newDescription).
For Field Configurations it's a bit confusing, because internally they are called "FieldLayout" (take a look at the URL when manually editing a Field Configuration :D). Use FieldLayoutManager#getEditableFieldLayout(id) to get the FieldLayout, then FieldLayout#setName(newName), then FieldLayoutManager#storeEditableFieldLayout(myFieldLayout).
For Screen Schemes, use FieldScreenSchemeManager#getFieldScreenScheme(id), then FieldScreenScheme#setName(newName), then FieldScreenScheme.save().
Use com.atlassian.jira.component.ComponentAccessor to get the Managers, as I showed in your previous question.
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