Plugs black on #1 and #2 cylinder (running rich) but not on 3 and 4. '82 Yamaha xj 550?

Bad sync would show up when idling. It wouldn't have that much effect once you opened the throttle. And the mains are probably fine since the bike is good at high range. If they didn't touch the midrange jets they should be OK. You could have a problem with the slides sticking on those fancy CV carbs. It could clear up at full throttle because you'd have more vacuum on them. The carbs on that bike are extremely picky about being perfectly cleaned and adjusted.