Hi @sampson
I have been working quite some time to setup a similar connection as you are, and I had a lot of similar issues. @vgaetera & @krazeh have been a tremendous help.
If this can help here is a link to my installation
Actually as I already planned to install this between 2 sites in different countries, I did setup all the encryption from the right beginning. WireGuard on top of OpenWrt has been the solution.
As when it will be installed I will not be able to easily access both sites at the same time, I did also setup another access through my iPhone form anywhere in the internet. So in case something goes wrong in my Site-2-Site I can still access both routers.
Have fun & it is very educational project. I'll keep a look on your DNS aspect as this is a point I haven't solved yet...