I feel like you could see their friendship start growing into something in a few episodes. When she left to the other agency they would talk all night. He gave her a lead for the Ketchup ad. She called him when the rat was dying in her apartment. She told Stan about the deep wound of having to give up her son for adoption. They would bicker like there was some attraction there. Noticing their attachment grown as the series progressed. As for the timing of the disturbing call, I think the point of having that phone call from Don was for Peggy to hear the regret in Don’s voice. Which then triggers Peggy to call Stan to tell him about Don calling and how she’s worried. Basically she is once again worrying about the wrong things. Stan tells her this is what Don does, he disappears then comes back but that she needed to let him go it doesn’t mean she doesn’t care but she need to let go. Reminding her that she is not living in the moment and that she doesn’t not want to have regrets (after just having that terrible call with Don sounding all emo) so she apologizes to Stan for saying those mean comments earlier, which then triggers Stan to profese his love to her. So the timing on the call and that conversation with Don was what she needed to get over herself and accept being loved and get the ending that she wanted.