Youre gonna get tons of opinions, but i go by this: Take it easy for 1 whole tank. Let it warm up, ride it for a little bit, let it cool down, repeat process for the whole tank. My experience, its enough for all the tolerances to settle in, and i havent had a problem yet doing that after 3 yearly rebuilds....but everyone has their own method.
AS for aftermarket parts, well, youre not actually breaking in the exhaust or carbs, its the motor (pistons, rings, gaskets etc) that "breaking in" refers to, so dont worry about when you break it in, or what ya got bolted to it. Just take it easy at first, and you shouldnt see a problem.
Have fun, take chances, go fast!