Ben,
Great news on the jetting! I guess it was just too rich after all.
I got my bike running smooth again, like it used to be and I wasn't dreaming that it wasn't right!
Not even sure what the problem was. Today I had the machine shop check my crank and it was just about dead on true less than .001 runout. So, I put the engine back together and back in the bike and now for some reason the vibration is noticably improved! I took it out for a 20 mile ride and my fingers didn't go numb at all, before I was stretching my arms out every 5 minutes to get my fingers to wake up... The odd thing is I don't know what the difference in engine assembly was. I had verified that my counter balancer was properly timed before so it wasn't that. The only things I know I did differently was I made sure to push the cylinder and head around to find the most centered position before setting the torque. There is a slop in the top end studs as they are long and narrow and simply can flex, so perhaps before it just wasn't as centered as it could be before it was all tightened down. The other thing I did different was I tried Mobil 1 15-50 oil, prior I was running Mobil 1 10-40. Not sure if the thicker oil is part of the smoother motor, but it definately makes the clutch feel less graby and more progressive. All that to say I'm not sure why the bike is smoother now, but I'm glad I kept at it until it was right.
If you decide to do the Trace tomorrow text me. If it's mid day, or early afternoon I might be able to make it down that way. (edited)