Ok, we will have to look into why the reference is null. Either the resource adapter isn't deployed anymore, or there is no managed connection factory for the archive. You can try and set a break point and see if that will give you an idea.
The view structure is better - however, the configuration part on the right side of the screen is still showing all the "old" values - like jndi name and so on. It needs to show the config-property's of the managed connection factory, like:
<config-property>
<config-property-name>myStringProperty</config-property-name>
<config-property-type>java.lang.String</config-property-type>
<config-property-value>JEFF</config-property-value>
</config-property>
The same when you press the resource adapter view.