Low Speed Carb Tuning
The fuel mixture screws are indeed located behind the brass plugs. The brass plugs must be removed to access the screws (click here for instructions). Be *very* careful about drilling out the plugs-use a drill stop. If you hit the screws with the drill bit, even for a moment, you risk running the screw down hard against its seat, destroying the screw and possibly the carb seat. Bad.
The fuel mixture screws deal w/ mixture at idle and a little bit above idle. They will determine off idle throttle response and extremely low idle cruising. Turn screws in to lean the mixture out, turn them out to richen the mixture.
Here are some rough guidelines to determine if you are running rich or lean at various rpm's. Examining the plugs is really the best way to get accurate results, but these guidelines will help you shoot for a direction (leaner or richer).
Idle and off idle
Lean condition: Poor off idle throttle response, idle that flutters a little after a throttle blip then slowly returns to the idle that you've set, popping back through the carbs when the throttle is blipped.
Rich condition: Off idle response may be good unless plugs are fouled from a way too rich mixture. After a throttle blip the motor will dive down below set idle and will either die if way too rich or may return to set idle if it can recover.
To adjust, run the motor until warm and idle is stable. Turn each screw in, one at a time, until the engine stumbles, then back the screw out until just rich of peak idle (idle drops again). Then turn them back in to peak idle. Repeat for each carb. If your screws are out more than 3 turns, the jet probably needs to be swapped to the next larger. The final position should be around 2.5 turns out on a stock set-up bike.
Pilot screw adjustment vs. Carb sync
The pilot screw adjustment and the carb sync are really different adjustments all together. If you had never done a carb sync it was probably good advise to do it once before fooling with the mixture/pilot screws .. or anything else. The carb sync is intended to equalize the opening of the carburetor throttle plates, (this is beneficial throughout their range of operation).
The reason you see different recommended mixture/pilot screw setting in the manual for the different models is because these bikes all have different size pilot air jets, (primary ... the one on the top of the carb ... the secondary pilot air jet is the same on all models and it hides behind the slide rubber inside the carb). Air from "both" of the pilot air jets mix with gasoline from the "pilot fuel jet" to produce the mixture that you control with the mixture/pilot screw, (except when you open the throttle a little .. because there is a bypass hole .. but that is another story).
The reason you'll find the screws set differently in each carb is because at the factory, (hopefully), they set these precisely using a CO meter connected to each cylinder via the little 1/4 pipe plugs you see in the factory exhaust pipes. These differences make up for the uniqueness of each carburetor and cylinder it is attached to, (rather unavoidable .. as minute as it might be). Cranking these screws out beyond where they might have been set originally will increase the CO readings for the respective cylinder, (make it richer at idle). Even though there might be other ways to achieve your objective ... this works pretty good for adding additional fuel at off idle ... and at light, (no load ), up to about 1/8 throttle throughout your mid-range, (which hopefully you will find beneficial).
There is a limit to this benefit and if you do more to your intake etc you may find you need to do something more substantial for you light throttle fuel requirements and do something different, (like make one of the pilot air jets smaller or the pilot fuel jet larger etc). As most of these bikes have the pilot screws set on the "lean" side for emission purposes you will hopefully benefit to some extent by backing them out a little. The models with the bigger primary pilot air jets etc are going to require a little more twist to achieve a comparable mixture result, (unless you are doing the ear routine or have your own $125 JC Whitney CO meter).