Hi Matt, When you download the source code for an app and self-host it, that app will display any embedded content, such as embedded story maps, the same as it does if you launch the app hosted in ArcGIS Online. So if you want to self-host a story map, you don't need to self-host the source code for any story maps or other apps that are embedded in your story (unless you want to apply customizations to them).
What's happening with your self-hosted code is that you are launching it via HTTPS, so any embedded content, like embedded story maps, won't draw unless they are referenced via HTTPS when embedded. So if I launch your self-hosted app via HTTP, the embedded content works OK I think, at least for the first two tabs: http://gis.co.scott.mn.us/2040/
To fix this, you can edit your app in ArcGIS Online to update the URLs of embedded content to reference it via HTTPS instead of HTTP. This will then work when the app is launched via your self-hosted code. This assumes that the content, i.e. the story maps, you are embedding support HTTPS. If your embedded content does not support HTTPS access, then you could still just deploy/share the URL of your self-hosted app using HTTP, like the URL I posted above. But the best practice is to support HTTPS where possible by only embedding content via HTTPS, to avoid the situation where content doesn't load .
Here are some blog posts related to embedding content like story maps inside story maps: https://community.esri.com/community/gis/web-gis/storymaps/content?filterID=contentstatus%5Bpublishe...
Hope that helps
Rupert
