I would first make sure the existing JdbcUsersConnectionRepository implementation is not suitable for you. Will save you a lot of work.
Assuming you actually need your own repository implementation, I would study how the existing implementation works. Notice how the Connection instances are created by ConnectionFactories obtained from a ConnectionFactoryLocator - they are in no way coupled to the repository layer.
In summary, you should not have to create a custom Connection implementation just to change the strategy for how connections are persisted. I would expect you to have to create a new UsersConnectionRepository implementation and that's it (internally it will need to define a single-user ConnectionRepository implementation type of course).
Core Spring Development Team