My oil stick is 1/2 over F. What do I do. Change oil. Loosen the oil plug? Suck some out sonmehow. Please help. 

Drip tray below bike, crack drain bolt, drain desired amount, check oil. Profit.

You pretty much answered your own question. Either let some oil out of the bottom, or take it out using something like a large syringe or a turkey baster.

Also, you're measuring when the bike has been warmed up, yes? Not when all the oil has had time to collect at the bottom.

I change oil every 2-3k miles and the filter every other oil change and put 3 quarts in each time.  When the filter isn't changed the 3 quarts fills it to the top of the flat on the dipstick which must be close to a half inch?  Not looking at it right now.  Never had a problem with that.