Does anyone know if the episode Johari Window was inspired by the real life story of The Elephant Man? I'm thinking it probably was considering they even called it Project Elephant 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 images from the victim's eyes (don't remember title) was based off of something actually used in the Jack the Ripper investigation.