Does Sai Baba still have a presence even though he left his body in Shirdi?

Yes, the text strongly affirms his continued presence. Chapter 43 states that after leaving his body, Maharaj became one with Brahman and now fills the entire moving and non-moving world in his true form. While he merged into an unmanifest state, he is said to still enjoy his true self and 'always keeps the devotees awake.' The scripture argues that since he is firmly imprinted in the hearts of his followers, his body cannot be said to have truly perished. His influence is described as proven, and devotees can still experience his presence based on the feeling in their own minds.