You can configure WSO2 IS 4.0.0 with an external JDBC users store.The problem is due to an issue with the instructions in the documentation(1) as some configuration steps are missing there.I have created the jira [DOCUMENTATION-17] to track this doc issue.
Please follow below steps to connect IS 4.0.0 with external jdbc users-store.
1) Change the UserStoreManager class to JDBCUserStoreManager from user-mgt.xml [IS_Home/repository/conf] and add the related database connection property to it as mentioned in (1)
2) Add 'passwordHashMethod' propert within JDBCUserStoreManager and set the value to 'SHA' or 'PLAIN_TEXT' in {IS_HOME}/repository/conf/user-mgt.xml.
Eg: <Property name="passwordHashMethod">SHA</Property>
3) Set value of the 'MultiTenantRealmConfigBuilder' property to 'org.wso2.carbon.user.core.config.multitenancy.SimpleRealmConfigBuilder' in {IS_HOME}/repository/conf/user-mgt.xml.
Eg: <Property name="MultiTenantRealmConfigBuilder">org.wso2.carbon.user.core.config.multitenancy.SimpleRealmConfigBuilder</Property>
4) Enable JDBCTenantManager in tenant-mgt.xml and comment out the config section for CommonHybridLDAPTenantManager.
Once you did above configurations,you'll able to configure WSO2 Identity Server to an external jdbc user store successfully.
(1) http://docs.wso2.org/wiki/display/IS400/Configuring+an+External+JDBC+User+Store