I've been thinking about this a bit more and I mentioned removing the physical elements but I forgot about one of the major factors that the Twilight Zone adds to the experience. The music, I can't think of any other piece of iconic scary music.
If Disney decide to go for a full retheme, the only IP that I think would be fitting would be Monsters Inc. The lift doors will open to different areas, one door will open to the The Himalayas and you see the Yeti, maybe a small quip that the yeti is moving in the scene. There is literally an infinite number of possibilities, all of which can be randomised.
The building could be rethemed to the Monsters Inc Headquarters:
For the basic story, the monsters are using us in their new machine to generate power by laughs, we go through the ride as normal with a list of terrible stand up jokes. Once the monsters realise this isn't working, we move through the 5th dimension scene as they decide they need to go back to their old ways and generate their power with screams. The underlying story is that we're helping Mike and Sully look for Boo, hence all the doors opening but they thought it would be an easy ride since we should only be experiencing some tame stand up comedy.
The loading area will be rethemed to the Scare Floor:
I've always loved the idea of the Monsters Inc coaster but I think this fits just as well.