First, I'd recommend taking a test ride with your helmet off to make sure you can tell that the sound is coming from the rear. If it's the chain, it should be coming more from the left side than the right.
I'd sure check the tire all over (especially the sides) for any scuff marks. Do the same for the inside of your fender and anywhere else the tire could rub. It sounds like you already did that. Then you could put the bike on the center stand and put the transmission in neutral (and the engine off), and turn the wheel by hand to see if there are any places in the rotation that seem a little stiff.
Freakinout gave some great advice. Everything he said to do is worth doing, even if it's not the cause of the noise. But I would suggest doing them one at a time, so next time when you hear this noise you'll know what it is.
You could also take off your rear brake pads, then go for a test ride to see if the noise goes away.
My gut feeling is that the problem is your rear axle. You can take off the whole assembly and take it to a machine shop, and they can fit you with new bearings and grease it up for you, and put in new seals.
And just for the record, it is a very, very dumb idea to ride without your helmet or without rear brakes.
Curt