One last thing...
I noticed the authenticator is manual.
Manual authentication can't be scripted; as it requires manual interaction.
It looks like you are using GoDaddy DNS, there should be a plugin to automate that for you.
It can when there's a manual auth hook, as there was with that guide.
The problem with that guide is that it tells you to use auth.acme-dns.io for your own production use, which really isn't how acme-dns is supposed to work.
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If that was the case, then why did certbot renew --dry-run work perfectly? 
Nah, don't sweat it. @rg305 notice a part of your setup which usually does not work very well, but forgot that there are situations where --manual works nicely as @danb35 also pointed out to @rg305 already, which is the case here.
The second part of @danb35's post I don't have experience with. I agree that having a dependency on a third party which also has the possibility of issuing certificates for your hostname (by "design" in the way acme-dns is implemented as it is right now) is not ideal. However, now that you have your certificate and you agree using the acme-dns service isn't ideal, you might try to implement your own instance of acme-dns instead of relying on the "third party" acme-dns service you're using now.
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OK thanks!!
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