You'll have to rejet and most likely make needle adjustments to the carbs if you want to run pods. If you ask me, you'll be a lot happier overall, and spend far less time if you just source the parts you need to use the stock air box.
My first sohc4 was a 400F, and it didn't come with the air box. I spent at least six months messing around with the carbs trying to get it to run just right with pods. I finally gave up and bought an air box setup on ebay, bolted it all up in about half an hour, and the bike ran perfectly after that.
