On top of deleting stories from dt_cms_schema.CMSStoryPubTracking and dt_cms_schema.SEOStoryLookup (see below), Craig M. recently discovered that one needs to delete "related" and/or "popular" stories as well.
Find orphaned SEO stories:
select distinct top 100 cmsStoryId as SEO_CMSStoryId from dt_cms_schema.seostorylookup seo where not exists (select pub.CMSStory from dt_cms_schema.CMSStoryPubTracking pub where seo.cmsStoryId = pub.CMSStory) and cmsStoryId is not null;