I believe any time there is some kind of performance problem with these bikes, a complete and through tuneup should be performed. You've done most of it, already. But, cam chain tension and tappet clearances aren't listed in your report. Also, I'd like some info on the spark plugs to; age, condition, heat range, plug number, proper gap. The color of the deposits on the center electrode insulator might also give a clue. Also, any differences in deposit color across the cylinders, might be interesting, as well.
A compression check would establish that the cylinder mechanicals are sound. And, that a burned or leaky valve is not contributing to low speed run issues.
Is the exhaust and induction system stock? Changes here can effect the separate carburator adjustments for different throttle settings.
Also note that the stock paper air filter can only be blown clean just so many times and then it must be replaced in order to get the proper air flow and restriction from it. The air filter is supposed to be replaced every 6K miles, according to the Honda manual. More frequently, if operated in dusty areas.
If you have addressed all the above, and there is still a problem, that leaves just carb adjustment. And, you want all the above done beforehand anyway so the carbs are tuned to a properly adjusted engine and not compensating for something mis-adjusted.
Do you know if the carbs have been syncronized?
If you have eliminated everything else but the carbs, the bike shop ought to stand by their work and finish the job properly by completeing the tuning adjustment.
Or, you can start with checking pilot screw settings.
At this point, you'll need to determine if the mixture is too rich or too lean.
Drive the bike at the throttle setting that annoys you (all warmed up), and apply partial choke. If the symptom improves you are too lean. If it gets worse with choke you are too rich. And now, you know where the adjustments should be made.
Report back your findings and ask more questions if needed.
Cheers,