It took me around 1.30 hours to solve. it turns out, Rocksmith Custom Song Toolkit wanted to read this random file in my Rocksmith folder. I never played it there, it was never there before. It was trying to get into this English(US) folder for some reason. IT wasn't letting Toolkit into it. For whatever reason. When I opened the folder that Toolkit was trying to use, I got 'Access Denied' I tried deleting this folder and nothing happened. In the end, and this is extremely game breaking (CDLC) I had to reinstall Rocksmith 2014 onto another drive because I cannot delete this damn folder. Reinstalling Rocksmith 2014 fixed it, because the template folder was reinstalled and hopefully fixed.
If I could suggest something to improve toolkit. Create backup folders for these folders that are used when generating CDLC. This was just a huge pain in the ass, the only way to fix it was like I said, reinstalling the game elsewhere. It was just because of one folder.
Strange. Making the new tuning fixed it. I just put in 'Custom Tuning' and it worked. Even after changing the frequency. I don't know if my Toolkit was outdated, because my SSD recently died with all my Rocksmith 2014 files on it. I downloaded the latest version of the toolkit today. I did make a new tuning before, but it kept changing to some random tuning. Now I got the outcome I wanted. Thanks for fixing the issue.