Let's review your DNS setup so far.
In Route 53, your domain name's Hosted Zone contains the following:
Name Server) record for your domain name. When a domain name is typed into a browser, the DNS looks to these name servers to help direct the request.
Alias) record. This record is used to direct requests of your domain name to GitHub's servers using their IP addresses.
Canonical name) record. This record specifies what custom domain will point to your true (canonical) domain.