I understand your pain, the science victory screen is the coolest... doing whatever I can to try to help you figure this out. About the parts showing up as made, IIRC, they only show up in the victory screen once each one is assembled. This is why I tend to do what you did, build all the parts and only then assemble the spaceship, so unless the AIs have spies in all my cities, they will never know close I am to the victory until it's too late. But I always managed to assemble, except one time that I tried to launch the ship AFTER winning diplomatically.