It seems I'm stuck with Main Quest 5 (found the daughter but need help) and Main Quest 3 (Trouble in the Undercity part 2). I can't talk to the Inquisitor since Heidi always asks her about the encrypted Datapad (which I already decrypted), which means I can't talk to the Governor as well (Servoskull reminds me I need to talk to the Inquisitor first). I chose to start the game as Halfway Heretic.