Thanks everyone! Yup following the new instructions @JMSolo posted here on the new ReadMe, I've gone from QuickBox v2.4.9 to v2.5.1 Going this route, along with the little notes here and there, a lot easier to know what you're doing.
I've upgraded both boxes I admin without any issues.
I'm still getting the
chmod: cannot access '/srv/rutorrent/plugins/filemanager/scripts': No such file or directory message on my personal box... but that could still be related to not having all the files that are supposed to be in there (and I'm not worried).
The other box I admin I have not touched it at all with this process, I figured I would wait until I got my box figured out before I attempted. So I did not have the same
chmod error like above on that box, but did have the the same line 456/460 error that @rumiat had. Though I kept just plugging through the steps, and seem to work without issue.
I've rebooted both boxes and they still seem to function without issues and are both on v2.5.1. Nice! If there is any logs or something to test if anyone needs, please let me know.