Does anyone know if the episode Johari Window was inspired por the real life story of The elefante Man? I'm thinking it probably was considering they even called it Project elefante in the episode.

You're probably right or it might have had some basis. Just like I found a story online that the episode Earthling (the one where people disintegrated to ash) was based off of and I know that the episode where they took the last imagens from the victim's eyes (don't remember title) was based off of something actually used in the Jack the Ripper investigation.