In your original post, you said : "The manual and the label on the case say the gear setup needs to be a 40-tooth on A, a 65-tooth at B, nothing a C (?), and a 55-tooth at D. There are no 65 or 55 tooth gears in the set or even on the lathe."
The 65 tooth is just an idler; you could have used any gear that fits in that space (with adjustment). No matter; the 55 tooth may come in handy some day. It took a while before I understood how change gears worked - it's just arithmetic (ratio between the spindle and leadscrew rotations), but it can be confusing.