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.
I am glad that you have got to the bottom of the problem with the lack of oil flowing. I thought it was a vac problem. If you can take the tube from the crankcase vent and try blowing compressed air through it, it may push any blockage up into the airbox, where you can clean the crud out.