I've used Route 53 as a DNS, but I didn't know, until you mentioned it and I checked, that AWS provides domain registration too. (It's hard to keep up!)
Usually, the two are separate. As stated here, you usually set-up the receiving DNS, copy the source DNS config to the receiving, then change the registrar's name servers to point at the new DNS.
It sounds like this is what you've done, mostly.
It might be worth your while starting a discussion on Slack.