Put the full 4.1 qts. in the bike. Start it up for a moment. Shut it off, give the bike a couple minutes to drain the oil back into the pan, then look at the sight glass again. I'm betting the oil will be right where you want it.
If for some highly unusual reason the oil went somewhere else, your oil light will let you know if the engine is starved for oil. It may stay on for just a few seconds (no more than 2 or 3 seconds) at your first start-up, then it'll go off. If it doesn't, shut the bike off.