When did Itachi plant his crow inside Naruto?
Itachi stores the crow inside Naruto in chapter 403, during the Itachi Pursuit arc.
Itachi used a shadow clone to talk to Naruto, who wasn't willing to listen. As such, Itachi was forced to use a Genjutsu in order to make him listen.

He uses a Genjutsu as a distraction:


And then the crow is stored (physically, I think) inside of Naruto:


This is corroborated by this Naruto Wiki page.