i just replaced my oil and filter. Added 2 quarts plus an extra glug from a 3rd.  When I dumped the old oil into the bottles, I had only about 1 1/2 quarts of old oil. My oil level before the change was just a little short of the top of the glass with bike level. Now it's over the top, but I don't think by much. Should I drain and refill?  It seems to run fine after a quick ride. I'd really like to avoid another mess.

As long as the oil doesn't appear to be foaming, or blowing excessively out the breather and into the airbox (pull the plug and drain) you should be ok.

but, if you're OCD, you don't need to drain, remove the timing port on the left and some will drain out.  put some tape under the port like a V or it'll drip off the bottom of the case.

Where is the oil level in the sight glass when the bike is on the side stand? It it is at or below the lower line on the sight glass, you will be fine. quite a few of us actually check the oil level with the bike leaning on the side stand, just make sure that it's at the bottom of the sight glass if you check that way.