In the first draft of the script, Lester and his friends weren't using Malkovich's portal as a means for extending their lives, but in a plot to take over the world in the name of Satan. Satan was the mysterious 'Flemmer' that the Merton-Flemmer building was half named after.
When Craig Schwartz first boards the elevator, the alarm stops when the stop button is released, before the door closes. But when Maxine boards the elevator to descend from floor 7-1/2, the alarm keeps ringing until the door closes.
When Lotte is chasing Maxine through Malkovich's subconscious, as Maxine drops into the school bus section you can clearly see someone's hand holding her skirt so she doesn't fall into the bus.
Driver:
Hey Malkovich, think fast!
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Maxine: Craig, I don't find you attractive, but Lotte, I'm smitten with you. I am... but only when you're in Malkovich. When I was with him last night, I was looking into his eyes and could sense your feminine longing.
Craig Schwartz: You see the world through John Malkovich's eyes. Then after about 15 minutes, you're spit out into a ditch on the side of the New Jersey Turnpike!
According to Wikipedia, screenwriter Charlie Kaufman always had Malkovich in mind due to his acting style and the sound of his name. Later, Malkovich took an interest in producing the film, but it took years until he was convinced to play himself in it.