No biggie buddy; just back all of the screws the same amount, say, 1/2 turn, then readjust your idle with the idle screw, which is nothing more than a 'master' air screw (take a close look and you'll see what I mean). When you do that, do leave #3 alone and adjust the others around it, so it's faster. Worst that can happen if you 'mess' with #3 is you either have a too high an idle or too low; easily remedied, since it's a 'closed' system (master/idle screw feeds all 4 TBs). And if you're really careless trying to lower your idle more than you can (could have happened to me, but didn't), you could back out the idle screw all the way, and possibly lose the spring, so DON'T do it. This 'master' screw is not really needed since you can adjust the air screws with it all the way out (mine is like this now), but makes adjusting your idle a snap when individual screws are within adjusting range, rather than having to mess with the individual air screws every time (kudos to Yamaha).
By the way, vacuum depends on your altitude, do don't try to adjust it; just make sure all 4 TBs are as close as possible to each other.
I also left #3 a bit too deep, and my idle can't be lowered more than 1,250, and I want it at 1,200 rpm, so have to go in there and back them out a bit too, which will do at the time I perform another TB synch after break in. By the way, reason I set the individual air screws as deep as possible is my bike restarts to idle speed immediately when hot, rather than restarting around 800, then slowly climbing to proper idle speed (like stock settings). No biggie at all, but the tinkerer in me wanted to make it better, so I experimented. Oh, and I marked all my screws before messing with them, but don't plan to put them back to stock, especially the 'unauthorized' ones, which were far from perfect. Hope this helps, and if you need more help, send me a PM.
JC