SAN DIEGO — This was a pivotal moment, a pivotal moment in the game, in Mike Pelfrey’s development, and the Mets pitching coach, Rick Peterson, sensed it. He ran out to check on his struggling pitcher, putting his hands on Pelfrey’s shoulders. Staring back, Pelfrey nodded every few seconds like a dutiful son, as if to say, “It’s cool. I got it covered.”.