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The main body is already combined with those two parts -- you don't need to worry about them. If you're curious about them, you can check out the engineering drawings -- 10016 and 10134. In the original Curta, they are forced fit parts that don't move in relation to the main body, so I combined their shapes with the main body.
Yes, if you print Main_Axle_and_Step_Drum.stl, you will still need the Main Shaft Bottom.