Update:
What ultimately fixed the minor stumble in the low throttle range was the fuel level in #2 still being a bit too high even after clear tubing and thinking it was perfect. After a ride, I noticed #2 spit out fuel from the overflow. So, I cleartubed it again and it was too high. Once that problem was resolved, and the needle clip was raised to middle position again, the stumble was completely non-existent.
Carb settings - 087a with UNI replacement filter in stock airbox: 105 mains, 38 slows, Needle clip - middle notch, IMS - 1.5 turns.
As said before I am NOT a short shifter and love to hear this exhaust. Given these riding conditions, on any given tank, I typically get around 35 MPG. I did a high speed run at the end of my 2015 riding season (60 degrees). GPS verified that I hit 99.6. I had to let off as I was quickly approaching a speed zone. But, from a stop all the way to 99.6, there was no stumble and I believe I could hit 100 - 105 mph.
Thanks again everybody for the help with this. Hopefully I'll be able to enjoy the bike more in 2016. Cheers!