You should really upgrade to a newer permissions plugin. I know a guy who knows the guy that updated pex and what I was told, was that he had to remove support for bungee (or something like that..) just to get the plugin to work properly with newer versions of spigot. There were also some changes to the way pex handles sql.
So if you want pex data stored in a database in order to use the same data across multiple servers and bungeecord, you're going to have problems and certain things are going to be a bit more difficult because of how arcane the software is. It was developed for servers over several years ago. It's not optimal for servers now.
I recommend LuckPerms or UltraPermissions. They're very easy to learn use and from my experience with UltraPermissions, it's extremely easy to set up a connection to an sql database. UPerms is mostly GUI based but has commands that handle the same tasks in case you don't like the GUI. It also seamlessly integrates with BungeeCord. It's a wonderful permissions plugin. It's premium, but I highly recommend it!
Now as far as your mysql database on cPanel... First make sure you can actually connect to it. Either through SSH or through another plugin. If you can't connect to it, then there's a problem with your mysql and/or cpanel configurations. I'm not very experienced with cPanel so I don't know how much I can help you with that.
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