Mac Mini Server Reset To Factory - Help With Fatal Error
In case anyone has searched this and had the same problem as me here was the problem. 

After a trip in to the apple store and some work on my own It turned out to be partly a broken sata cord inside the mini as well as the raid partition setup. Once the apple store employees helped me find the sata cable that was causing the error I realized the final problem was that one of the raid slices was set as a promoted drive.

The reason I couldn't tell this was the actual problem was an unrelated separate problem which turned out to be a broken sata cable. Once that was replaced it was fairly easy to see that one of the raid slices needed to be demoted in order to remove both partitions and truly wipe the HDD.