My bike has aftermarket clutch and brake lines which are noticeably longer than stock. They're actually a little too long, but its not a big deal. The fast idle cable is stock since it had obviously never been removed from the throttle body when I pulled the bike apart.
The problem isn't the lines, its the handlebars, levers, or master cylinders hitting the fairing (or tank). I'm going through this right now with my project bike that has cbr600f4i forks and bars on it. They aren't angled correctly and don't have the same rise, so they either hit the tank or levers start hitting the fairing.