Regarding pods, it's really not about airflow until you rev the engine near or above red line.
The most significant effect of them is the change in pressure experienced in the carb throats. Since the carbs deliver fuel at a rate determined by the pressure differential between the carb throats and what exists outside the carbs. Changing to pods and shortening the inlet duct, greatly diminishes what fuel the carbs deliver, if they are still set to factory specifications. Honda adjusted the carbs to the parameters that the stock air box presented to the carbs (as well as the exhaust pressure reflections). So, changing the intake and exhaust parameters requires finding new settings/sizes for the carb fuel delivery internals, which are very unlikely to be equal to book values.
I expect the CB650 to be particularly sensitive to induction and exhaust changes as these bike were introduced during the EPA's initial crackdown period on motorcycle exhaust hydrocarbon emissions. So, Honda fine tuned the carbs to balance properly with the production induction and exhaust.
It's not impossible to make changes "work". But, "working well" is another matter, requiring proper test and measurement techniques and a pretty thorough understanding of how the whole system works. Alternately, you must be pretty darn lucky.