Best do one change at a time. Isn't stock position 4th groove from top for the needle clips?
Anyway with the pods and pipe change, those carbs will need to go through a rejet procedure.
Test rack WOT run at throttle setting, plug chop, read plugs, make adjustment, repeat until correct plug deposits. Then you can do the same thing for 1/2 throttle to find the correct needle setting.
Then adjust the pilot screw for proper throttle response.
Saves a lot of time and work using a dyno. But, then there is the money it costs. (Which will probably make the "deal" you got on the modded bike purchase not look so good.)
I guess there is still the random change and try technique.
Or, return the bike to original configuration and use the carb setting that Honda specified. Done, and go ride!
Cheers,