How do I change permissions of folders on a hard drive from a booted USB drive
For anyone else that has this issue, the guys over at AskUbuntu solved it for me.

You can find the answer, along with other good answers, here:

https://askubuntu.com/questions/563054/how-do-i-change-permissions-of-folders-on-a-hard-drive-from-a-booted-usb-drive