Sorry for the lack of response. Here's what I did to get the bike running well.
1) checked all boots (all were fit well and adjustments did not make any difference)
2) checked vacuum lines (no leaks)
3) replaced air filter (no improvement)
4) used a digital laser thermometer to check header pipe temps. Noticed cylinder 1 is much colder (50-60 degrees) than cylinder 4 and cylinder 2 and 3 are aligned well. So that tells me something is wrong with cylinder 1. Checked spark plug to ensure proper torque and ignition wire was tight, no difference. I then began to slowly adjust the air/fuel mixture and everything started to start aligning up. In the end I needed an adjustment of about 1.5 turns out on cylinder 1 which resulted in no more popping, much better power, and overall made the bike run great.
I took her out for a quick spin and 1st gear roll-on lifted the front without any input from me, so she's back to running right again.