StructuresBecomeConfiguredFix's CONVERSION_MAP is invalid, as it is setting the fallback for ruined_portal to ruined_portal_standard. There is no "ruined_portal_standard" inside BuiltinStructures, so it's converting to a structure that doesn't exist. It should default to "ruined_portal" instead, judging by the field name "RUINED_PORTAL_STANDARD".
Can't provide world, it was already converted.
Can confirm, attached game log and pre/post-upgrade world folder.