"Rename"? Most if not all of the IDs would not have existed before so there is nothing to rename... There may be a few generic classes/ids that will need the selectors in their rules renamed.

As you found, copying the /includes/ folder over the existing site's /includes/ will only replace exact duplicate paths. If you have any override copies of files in the mod already, they would need to be winmerged to keep your existing edits. Most if not all of the mod's files will be new and unique.