It took several days to work through the issues so I wanted to put this out here as a help to anyone who has this same issue in the future.
I followed the instructions in the docs to deploy my website to github pages: https://docs.expo.io/versions/latest/guides/deploying-websites/#creating-a-build
This worked and I could view my webapp on https://.github.io/
However, when I attempted to use a custom domain in the github settings I continued to get a 404 error with issues related to the Manifest.json.
The problem is that you need to set a baseHref which you can do so by updating package.json with the following:
Hopefully, this helps someone in the future.