Deleted Scene: The Amazing Larry moment and the Boomerang Bowtie were both explained in cut footage that can be found on the DVD.
Survivor Guilt: During the scene when Pee-wee is wheeled out of the bike shop on a gurney, actress Elizabeth Daily's face went completely white. After filming the scene, Reubens asked her what was wrong and she replied to him that the scene had brought back painful memories of seeing her then-boyfriend, Jon-Erik Hexum, being wheeled off of a set on a gurney after accidentally and fatally shooting himself.
In exchange for Elvira playing the Biker Mama, Reubens was supposed to have repaid the favor by appearing on her weekly syndicated horror show, Movie Macabre. Ironically, John Paragon (the actor who played Jambi the Genie on Pee-Wee's Playhouse) was also a regular on Movie Macabre, in which he played "The Breather", a disembodied voice who'd call Elvira during intermission and would tell bad jokes.