So what I think is going on is that the NSA archives packets it can see in transit, but doesn't necessarily know who all the endpoints are. (It probably has a VERY good idea most of the time.) When someone becomes of particular interest they can execute a warrant on Google et al and get more detailed information on a specific target which lets them make better use of data they've already got.
The key thing they're doing is, fundamentally, logging packets that they can see going past any number of bottlenecks in the internet, which should have been perfectly obvious that they would try to do from day one. This alone is enormously powerful and all the extra info from service providers is probably only icing on the cake. If you can be identified from some cleartext comms somewhere then all you other dealings have been archived, and can be correlated, and then decrypted and traced back to you posthoc.