To me it sounds like an ignition issue. Remember that the voltage required to fire a spak plug is much higher when the engine is loaded. Is the bike even worse if you lug it and try to accelerate? I wonder about resistor caps on the plug wires or a bad coil etc.
When the engine RPM gets up a bit and the load on the engine decreases the voltage required to fire the plug drops. If any part of the ignition system is just marginal it could run OK when the load on the engine is moderate or light but balk when the loads are heavier like when it pulls hard at low RPM.
A scope would be the best way to see if that is the issue. A backyard mechanic can hook a timing light to one plug wire at a time and have a passenger watch the light flash to see if the light flashes irregularity is in sync with the engine. You would have to do it 6 times. Once on each plug wire. Is the problem worse when riding 2 up? I would think it would if the ignition is the issue, but maybe not in lower gears.
You might be on to something huge here because that is exactly what my bike is doing. At low RPM under load (lugging it), in any gear (even 1st), she spark knocks with 87 Octane that can actually be heard, whereas with 93 Octane she jerks without the distinct spark knock sound. Yet the jerking and spark knock sound are the same. This is why I was suspecting a lean condition either caused by a faulty carb (left side) or a vacuum leak. Then again, a jumping plug wire might produce the same thing.
And to answer your other question, yes, she pings worse with a passenger on the back, but within the same RPM range. Sometimes, when with RPM's high enough, the bike will not jerk, but you can hear it fluttering inside the left intake manifold. My timing light broke so that is why I haven't done that test yet.
I'll see if a friend has one that I can borrow.
I'm leaning towards an ignition problem. Oh, but all of the plugs looked beautiful; neither white nor black; they all looked really clean and I've never seen plugs wit almost 40,000 miles on them look so good. I would assume that a spark problem would lead to fouled plugs.