I am writing this in response to the question on this thread
97 Advice Offered and Advice Needed
I am unable to post on that thread and I can shed some light on the problem.
The sub air filter is not connected to the air box in any way. It is connected to a breather pipe that connects all four carb tops. The purpose of this breather is to allow the flow of air both in and out when the carb diaphragm expands and contracts. If the filter is blocked then the carb slides will work but the diaphragm will be in a vacuum and won't move.
It is located on the right hand side between the frame rail and air box. It should be cleaned whenever the air filter is replaced. You have to unclip the base and remove the foam element, clean it in solvent, re-oil it and replace. Beware of over oiling it as this stops the airflow and can also cause problems.
Hope this helps?