I am remembering the stock motor when new, it always did the rough jerky stuff when it first started out.   I remember watching the gas tank jerk in its rubber mounts when first accelerating away from the stop sign at the end of my street and again at the end of my neighborhood, so it took a minute or so to go away, always.  It happened when I short shifted, too.

Miles on the odometer is what helped the issues.   So did modding the carb and airbox and exhaust system.   But it was mostly just piling on the miles and learning to run the engine up some in RPM before shifting.

What stopped it completely was the stage 2 cam which causes you to HAVE to run extra rpms at each gear -- so the issue can be stated as you lugging the engine somewhat at the start of each gear.

Try intentionally running higher rpm shift points and see if it helps you out.

 
Dennis,

Did your new air filter ever come in?   Did replacing it affect your issues?

Oldfeller, I did replace my air filter with another stock filter but it change anything.  I gave it one shot of Sea Foam a little while ago and I don't think that really improved things but I'm planning on giving the Sea Foam another go today.

My plan of attack is to check the petcock next.  If that isn't conclusive, I'm going to think about the white spacer mod.