Kabuto is older than Itachi, currently Kabuto is 23-24 years old, while Itachi is somewhere 21. So when Kabuto was 5-8 years old at the orphanage, Danzo could not have Shisui's eye in any way, since Itachi was practically a newborn at that time and Shisui was also still a child, he died only ten years later. And Orochimaru is still Konoha's Shinobi at the time when Kabuto lives in the shelter, because Orochimaru has the clothes of the village of Leaf and Konoha's bandage. And Orochimaru left the village after the appointment of Minato Hokage, or maybe at most after the death of Minato, that is, Shisui was still a child in any case.
