Yep, I support what Leon has said about using Softaculous. Yes, sometimes it might work, but it seems to always have some kind of problems. The real problem is that Softaculous is acting as your "moodle admin" who is doing a lot of stuff "behind the scenes." Then, when someone has a problem, we (meaning folks here who try to help) have no clue what your "moodle admin" has done, so we are unable to provide much help. This is why you will often get a reply like "talk to Softaculous," which is equivalent to "take to your moodle admin."
Also, it is not surprising that Softaculous didn't work. There were some significant changes between 3.5 and 3.9.
So, learn to install Moodle on your own and do updates on your own.