In the room with the Obelisk of Doom the Mara letters are the initials of the Imagineers that worked on the ride.
In the film room, right after you make the first turn you can look up between the boards on the scaffolding to see a hidden Eeyore (You will need a flash light to see it). This was put here because the Indy ride building was built on the former Eeyore section of the parking lot.
The letters and numbers on the EMV vehicles are actually the initials of Imagineers and their birthday with the month and the day. The last digits are the number of the vehicles from 1 to 16.
In Indy’s office there is a Life magazine with Mickey on the front.
When you first enter the room with Indy’s office you look up to the top and see cargo boxes with writing on them. The writing is from the first Indy movie, Raiders of the Lost Arc, and was on the cargo box holding the arc of the covenant.
On the left side of Indy’s office there is writing that says send to Club Obi Wan, this is a night club from the Temple of Doom movie.
In the mummy room on the ride itself, the first skeleton as you enter the room, on your left has a Mickey Mouse hat on that has the name bones.
The "three rooms" you choose from are not three different rooms but only one with facades that move on the from to make it look like they are different
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