I am working a new version of AdvGen CMS. I found the ApplicationUserManager has to use their Entity Framework. I cannot just build our own ApplicationUserManager to switch a different ORM layer. You have to build your own IUserStore like this:

public class AdvGenUserStroe : IUserStore

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And then build your own ApplicationUserManager which is using this custom user store.
This is the only way to have a Custom ASP.NET Identity in MVC 5