@dreamingofadmin I think first step is to get access to your dashboard.
In Cloudflare, do you have an entry for my.domain.com to your server IP (DNS A record) ? If not, add this manually.
Wait a bit.
Access https://my.domain.com . If it's asking to accept self signed certs, accept them.
Once in dashboard, Domains -> Sync DNS . This will add all the DNS entries.
Then, Domains -> Renew all certs.
Please let us know what is failing and where.