Welp, after 3 days, the defrag only made it to 78% before it stopped defragging, and from what files it was trying to fix, it seemed like it wouldnt finish cuz those files were most likely ones it didnt have correct permissions to use, so I stopped it.
It went from 71 to 31GB of defragmented files, and now everything seems to be working just fine. i wish windows could use EXT4 file system like linux so I wouldnt have to deal with this crap q.q
If it was a permissions thing, make sure you right click and run as administrator.