So it seems that the files I transfered for the backup were corrupted a bit. I had used Filezilla but absolutely forgot to switch to binary transfer. I was about to upload again when I decided to call GoDaddy. We have a fully managed server so after 15 minutes of explaination I was informed of cpanel to cpanel restoration. My tech did everything and sent me an email two hours later and viola! He helped with just about all aspects of our system. Anyway all is good now and thank you so much for the reply and answers to my problems. Oh and the original problem was a brute force attack with some malware being injected into our server that made Moodle go absolutely bonkers. All security issues were addressed.