Will the shuttle be running after the Afterparty?

Yes

Shuttles will depart from Rosarito Beach until 3am. Afterparties begin immediately after the closing act, around ~12:30/1am.

Both the Papas&Beer and Bombay Afterparties are connected to the festival grounds (<5 min walk to the entrance of Papas&Beer or Bombay). Meaning, you can attend the Afterparites after the festival and take the Shuttle, up until 3am. Shuttles depart from Rosarito Beach Hotel (<5 min walk from Papas&Beer and Bombay).