Mexico issues this press release last July:

In response to a formal request for extradition by the Government of the United States, through diplomatic channels leading, and derived from a process of analysis and diagnosis of such request, on 29 July this year, the Attorney General's Office obtained -from Third District Judge of Federal Criminal Proceedings in the Federal District -formal detention order for extradition of Joaquin Guzman Loera.

During the analysis conducted by the PGR it was verified that the application meets the requirements of the Extradition Treaty between the two countries and with the requirements mandated by the Mexican legislation.

Here is the transcript of the Attorney General's statement at the press conference last night, describing those responsible for his second escape, recent efforts to capture him and the details of yesterday's capture.

As to his July, 2015 escape, I filled in the names here. Here's my recap with photos of yesterday's capture.

As to Chicago, a 9th Superseding Indictment was returned in April, 2015 (Docket No. 422) and unsealed in September, at which time the Judge re-issued arrest warrants for El Chapo, his son and El Mayo (Ismael Zambada-Garcia). The docket entry for El Chapo and his son states:

ORDER as to Joaquin Guzman-Loera, Jesus Alfredo Guzman Salazar: The Clerk of Court is directed to re-issue Arrest Warrants for defendants Joaquin Guzman-Loera and Jesus Alfredo Guzman Salazar. The Clerk of Court is also directed to provide the Government with three certified copies of the 9th Superseding Indictment and three certified copies of the Arrest Warrants for Joaquin Guzman-Loera and Jesus Alfredo Guzman Salazar. Signed by the Honorable Ruben Castillo on 9/28/2015. Mailed notice/ (ym, ) (Entered: 09/28/2015)

I would assume Chicago has filed an extradition application by now, but that's just a guess. (Maybe the reason they needed three certified copies and decided to unseal the Indictment was to enable them to submit it to Mexico as part of the application.) Normally I would say it's crazy to think he'd go to San Diego to stand trial in a case brought more than 20 years ago, but since Mexico just extradited one of his co-defendants in that case three months ago, I no longer discount the possibility. Here are more details on the San Diego extradition request. The Government's version of the facts in that case are in this pleading, filed in 1996.