That's another interesting thing about my conk, in the 5 years of changing oil it has Never been able to hold a full 3 quarts without over filling, even with a new oil filter, i get pretty close to three quarts but if i put the last bit in it will go over the sight glass and i never liked that, i like to see a little gap at the top of the glass, and yes i always pull both plugs, now when i first bought the bike i didn't know about the second plug so on my first oil change i can see why 3 quarts would be a little over fill because there still a little bit in the engine. and yes i like many other have over filled slightly to where the glass would be solid black witch not a good thing as Vic Salisbury said it blows oil into the airbox and it becomes a mess.
what i do is put in just over 2 1/2 quarts then rid it a mile or two and let it sit overnight on the center stand and check it the next morning and finish filling it up to where i want it.