The leveling system isn't it's own plugin, it's included in the main crafting system plugin.
You might be talking about the experience display plugin, which added a command to the menu to show all of your crafting experience, and the reason you couldn't find it might be because you didn't know the name of it.
As for your other question: The MZ and MV versions of the plugin are essentially only separate because when MZ first came out, I had to make an entirely new plugin for MZ. At a later time, I split the plugin into the core, and the MV and MZ branches of the plugin are an answer to having to deal with the different ways that some functions work, such as drawing windows.
With that being said, the only reason I left them as separate plugins is because there was no good way to handle a merging of them. If I deleted the MZ version off the store and included it with the MV purchase, people who'd bought the MZ version wouldn't have access to the download anymore. Same if I did the other way, if I merged the MV version into the MZ version, the people who'd bought the MV version wouldn't have access anymore.
I didn't want to have to deal with trying to hand out keys after the fact for the other version.
What I can do for you in this case is a coupon code for 50% off the MZ version if you already own the MV version. This isn't specific to you, but it needs this specific link to work, so feel free to share it to others if you know anyone else who's also in the same boat.
Good luck and godspeed.
~Ramza