If you are going to go with pods, you will need to re-jet. Or, you can cover the pods with T-shirt material to get the small amount of negative pressure needed to raise the pucks, it will be trail and error until you get it right.
So you don't have anything on the carbs now at all? A stock airbox with the filter is probably best as that's the way they were engineered originally and pod filters can work, and even velocity stacks have a screen to keep debris out but like dirtdigger says you need to have something there to protect your motor and get them to function properly.