Happy to read that it has worked. 
But: I don't think it's a problem of your system.
- The error message from Letsencrypt is wrong, so it's not really a dns problem (or)
- some name servers of Godaddy had blocked some of the secondary validation servers. May be temporary / high number of queries, that looks spammy
You domain uses the same name server.
The GoDaddy name servers have one problem: Sometimes it's terrible to find all ip addresses of these name servers:
| A | Info:: 27 Root-climbing DNS Queries required to find all IPv4- and IPv6-Addresses of 2 Name Servers. |
|---|---|
| A | Info:: 27 Queries complete, 27 with IPv6, 0 with IPv4. |
| A | Good: All DNS Queries done via IPv6. |
| Bad (greater 8):: An average of 13.5 queries per domain name server required to find all ip addresses of all name servers. |
13,5 is a bad result. Good name server configurations have 1 - 3. My own domain - 15 queries to find 5 name servers = 3 per domain name.
If it requires a lot of time to find the ip addresses of the name servers, that may produce a global "can't find your A-record".