Getting a smooth transition from circuit to circuit with pods can be a trial.
And, as Hondaman has stated, pods can cause turbulence at certain RPMS, no matter how spot-on your jetting.
The stock airbox has built in velocity stacks. Most peopel will tell you "If it runs good, leave it alone.."
Also, some people have said that just going with a high flow filter in the stock airbox will net you the same gains as pods, without the downside of pod turbulence.
Still will have to rejet, but probably no more than half a size up, unless you make other breathing mods to the bike.
(I have to run 125's with pods and only a tiny increase in exhaust flow.)
p.s. by the way, i'm currently working on a design to replace the stock airbox, with something that is actually an upgrade.
http://www.sohc4.us/forums/index.php?topic=26342.msg271600#msg271600