I just did mine with the tool from F.A.S.T. (This is for PWK carbs so it may differ slightly from factory Mikuni's)
Carb Sync at idle
-First, remove airbox or pod filters, exposing carb opening, to allow the use of Sync Tool.
-Start by screwing in the cable adjustments on the carb tops
-Next, set idle screws for desired RPM's at idle
-Use Sync Tool to check vacuum on both carbs; adjust one carb to match the other until both carbs read same number on Sync Tool. (Back and forth several times to be sure)
-Once carbs are Synchronized at idle, move onto mid-throttle Sync, to achieve best mid-range throttle response.
Mid-Range Sync
-Remove thumb-throttle cap at handlebars
-Screw in cable adjuster at thumb-throttle mechanism to give cable as much slack as possible
-Use a screwdriver bit or anything of the appropriate size to wedge into the thumb-throttle mechanism to hold the throttle at a mid-range RPM (don't go too high)
-Use Sync Tool to measure vacuum from both carbs and carefully take up cable slack via the cable adjusters on carb tops, back and forth several times to be sure they're accurate.
-Once both carbs are synchronized to your liking, take up the remaining slack in cable via the adjuster at throttle mechanism, leavin approximately 1/8'' of freeplay.
I hope this helps and is as thorough as I intended it to be.