Did Amir Shakkar complete his nine-month stay in the Chavadi as ordained? What happened towards the end?

No, Amir did not complete his stay as instructed. Chapter 22 recounts that after some time, Amir grew tired of being confined to one place. The constant stay began to feel like a prison to him, and his mind started to long for freedom and a change of scenery. Giving in to this feeling, he made a decision without Baba's permission. He abandoned his post at the Chavadi and traveled to Kopergaon, where he took up residence in a Dharmashala. It was there that he immediately encountered a dying Fakir, setting in motion a new series of events.