-_- given that "function" in evolution terms can be as shallow as "makes organism more attractive", the answer is yes. However, you are applying a demand that nature doesn't need to follow. As long as an added part isn't much of a detriment before reproduction, it can persist. Heck, that's how Huntington's disease persists in the population; it doesn't matter that it kills people, it kills them after they have already had kids, so natural selection doesn't weed it out.
Irrelevant as long as it still runs. Heck, all life on this planet has variations on the exact same "engine". I challenge you to find a single organism that doesn't perform glycolysis. The citric acid cycle in no way impedes glycolysis even if it were half formed. Same goes for the electron transport chain. Evolution doesn't replace the engine, it just adds to it. A car equivalent would be having a second engine being built on the side of the first one rather than the first one being replaced. "But Sarah, that wouldn't fit in a car", cells can grow, cars can't, deal with the fact that cars and airplanes don't have all of the same qualities as living organisms.