I'll take a stab since there's no responses yet. I have an '84 500, but I suspect the procedure is the same. First, get a synch tool. These come in two varieties that I know of: mercury tube and analog dial (there may be digital out there now, too).
Second, read other online sources, like this one or this one for general guidlines in doing synchs. However, your cylinder order of synching will depend on your bike, which may be what you're really asking. For that, I highly recommend a service manual; they're a good investment for any do-it-yourselfer.
You might also try the fj600 owners group on Yahoo. Not much activity there, but worth a shot nonetheless.
Dragging knee is for the track, and dragging tail is for the lot. --Kane Friesen
When you're in a car, you're watching a movie; when you're on a bike, you're in the movie. --Robert Pirsig