It works! Here's what I did:
In my ISPConfig settings for the server, I created 2 Co-Domains. ns1.domain.com and ns2.domain.com.
In the DNS Manager, I made sure that I had A Records for ns1 and ns2 that pointed to my server's internal LAN IP address (ie. 192.168.x.x)
Then I went to GoDaddy, selected my domain name, scrolled down to 'Domain Host Summary' (don't worry about the Nameserver Summary yet) and added only the first host, ns1, that points to my external IP Address. Than I clicked Save Changes. I waited about a minute for the changes to take place then clicked on the '+' next to Domain Host Summary to make sure the changes took, then I did the same process again for ns2.
Now, once both ns hosts were entered, I clicked on the '+' next to name server summary, then on 'see details or modify' link, and added 2 nameservers. I was using zone edit, and wanted to keep those ns entries in as backups (during testing), so I moved them to Name Server 3 and Name Server 4, and added my ns1.domain.com in Name Server 1 and ns2.domain.com in Name Server 2.
The 'unavailable' error you were getting (and I was getting before) was because our Nameservers aren't fully qualified and GoDaddy won't allow it. But, if you put the info in the Domain Host Summary, GoDaddy will allow your own DNS.
Once I got all the info entered... I had to wait about 3 hours before the changed took effect and browsing to mydomain.com picked up the new NS info... it wasn't instant. (I guess 3 hours is good, GoDaddy said it could take up to 2 days.)
Hope this helps.