Why did Amir Shakkar agree to stay in such a terrible place, and for how long was he there?

Amir Shakkar stayed in the dilapidated Chavadi purely out of obedience and faith in Sai Baba. As Chapter 22 explains, despite suffering from rheumatism and finding the conditions miserable, he accepted Baba's firm words as his medicine. His internal faith was certain, which allowed him to endure the external hardships. The text states that a stay of nine months was ordained for Amir in that very place, where he resided on alternate nights as commanded by Baba.