I looked in Tokotah Alley numerous times right where I knew it would(should be)! Found out you cannot just "link" to Tokotah Alley through the Nexus. You have to go to your own personal Bevin and use the Bahro stone in the book room!
Now I am trying Minkata and having problems, but I'll get it!
The City Locations in the Nexus link you to the public instance of the City.
The Bahro stone in your bevin/hood, the Great Zero Antechamber book in your bevin/hood, the City Bahro stones spread throughout the five Prime Ages, the Descent (now "D'ni-Tiwah") Bahro stone in Tokotah Alley, the Kadish Gallery book in Kadish, the Sharper's Office book in Teledahn, and the K'veer POTS portal in the Cleft link you to the bevin/hood instance of the City. As you link through each of these Bahro stones, books and portal, a page is added to the 3rd brown D'ni book on your Relto bookshelf, which also links you to the bevin/hood instance of the City.
The odd exception is the link to the Great Zero Courtyard AKA Rezeero. This bevin/hood instance is only accessible via the Nexus Personal Ages menu; no page is added to the D'ni book in Relto.