This is just information for anyone considering multisite install. It comes from two weeks of testing every configuration I could possibly achieve, and nights of research on codex and discussions with godaddy.
For one, my experiences dictate that what ever domain you are going to enable it must be the PRIMARY DOMAIN (i can't stress this enough!, it just makes it all go like a piece of cake with no hacking) associated with the hosting. This ultimately was the answer with godaddy. Also it was the answer with HostGator. All the problems were easily solved upon using only the primary domain.
As for using subdomains, make sure your host allows wildcard**. So at this point I have subdomains working with Host Gator and sub directories with godaddy.
I have done this enable/install numerous times at this point so if anyone needs help email me. I am going to do a screen recording with current version of wordpress if anyone needs it just email me. I'll post a youtube/vimeo link here tomorrow.