Hey there,
Because we rewrote so much during the time between the github version's last release, and the first release on the Asset Store, the two versions don't share a whole lot of code. This will unfortunately make it extremely difficult to upgrade straight from one to the other. Even things like object and prefab hierarchies vary from version to version.
I'd suggest treating the new version as an entirely different asset (it pretty much is at this point).
Of course, nothing's stopping you from (backing up your project and) trying to migrate anyway, but I can't guarantee that much will carry across without a fair bit of work. Sorry about that.
~Declan.