I havent done mine yet so I cant speak with experiance weather or not you have the chain the right way round? But if you have and it still dosent line up, and its only by a link or so, I'd say its perfectly feasable that your old chain had stretched, or you have jumped a tooth like whats his names did on one of the threads below yours. To tell if your chains stretched just lay it out next the the new one. I know its sounds weird a chain stretching but it happens all the time and is caused by wear in the link pins.