Surely if some well funded organisation (Eve) were to install a similar number of relays itself, then it is reasonably likely that for a given user a packet would eventually travel across relays solely owned by Eve, and at that point Eve could map a Tor address to a physical IP?
Operating 6000 nodes in a manner unlikely to cause suspicion , and correlating packets across those nodes, is a massive undertaking, but it seems that it would be well within the means of e.g. NSA.
Would this work, or am I missing something fundamental about how Tor works?