Okay did grep, nothing came up. So there's no unexpected base64 in the files. Hostgator is saying that there are connections being made from the site. MyBB says the database is clean. I really don't think it's the host because I can upload absolutely anything, including MyBB in another directory and it loads perfectly. This is really annoying :/
Check your PHP memory!
Do you have dedicated IP or shared?
Disable all plugins and give it a try!
Reduce the number of outgoing calls like to Jquery and stuff!
Use Anonymous JavaScript !
Use GZip Page Compression?
Pretty sure it's a shared IP.
I've managed to fix it though! Still don't know the root of the problem though.
I uploaded a fresh MyBB to /forum and set it up with a new database. Then edited config to the old database with everything in it. Uploaded theme images to the new folder, and copied the CSS over. Done. Everything works perfectly in the /forum directory. However, I tried to copy it over to the root directory and it went back to 30 second loading. Left it in the /forum directory and then changed the root index to a header location of /forum and now it works perfectly!
Still don't understand why in the root it takes 30 seconds and everywhere else it doesn't but it's working now. Thanks for everyone's help and suggestions it's really appreciated.