IMO - and it is only my opinion . . . yes, you should get the stock air filters back on, the engine was designed to work best with those. HOWEVER, that said, if the PO rejetted the carbs to accomodate the PODs, you will need to look into getting the right sized jets in there.
Why do people use the pods? Have you dealt with the original airboxes? They're a PITA to get on and off - pods are easier, just little clamp-on filters. I almost did it on my 360, glad now that the bike shop didn't have them in stock.
There will be people around much more knowldgable than I to welcome you and help. In the meantime, download your manual from this site - it will be indispensable.