Don't worry Doug, I'd be ranting myself if experiencing same on my motors. Wanted to perform an experiment taching a 3 cylinder Yam 85 individually but my friend is out of town for quite a while. It's very difficult to fine tune a 3 and up cylinder carbs to work spot on and achieve a near perfect idle rpm, luckily for my peace of mind only run 2 cylinder single carbed motors. Would definitely go crazy adjusting 3 carbs at the same time.
If the tach is reading correctly, warm the motor on muffs for say 3 minutes, install the pick up wire on upper ignition coil wire and write down on a piece of paper the idle rpm achieved, remove the pick up wire from the first ignition coil and perform the same for the second and third ignition coils. Compare them to each other, are the 3 idle rpm readings the same ?
If not and with notorious rpm readings differences probably could adjust each pilot screw individually to read even or close to each other ? If works Bingo. BTW this is an experiment. Rough idling could be blamed for too much carbon buildups inside the combustion chamber, carbs badly adjusted or a combo of both situations. Remember that one of the carbs has a larger jet that what the parts manual calls for, if adjusted with same number of out turns as the other two carbs that cylinder theoretically will receive more fuel than the others, if so will need to adjust it to the lean side to compensate.
Tell tale won't peed much if running the motor on muffs due to too much water loss on the ears, deficient house water pressure, a combo of both situations. Motor should peed much better when running at open water. Never seen a motor to overheat at idle on muffs, unless impeller is shot, water hose popped off from muffs and weren't aware of that...
Happy Boating