You should try decapping the stock airbox first (assuming you install a K&N filter)
I was hesitant to do it, but I now wish I had done it months ago. I was astounded at the difference opening up the stock airbox makes.
If you go to an aftermarket air intake, you will have to re-jet. If you decap, you will have to re-jet. Either way, you will have the initial investment for a jet/needle kit. If you like the results from the decap, you can save a fairly substantial cost on an aftermarket intake. Also, you will need to consider that some aftermarket intakes do not take into account the crankcase breather or the idle screw. You will need to find solutions to those oversights. With a decapped factory airbox, you simply plug them back in where they originally went.
I followed Bassdude's how-to thread. It worked out very well.
http://www.vtxcafe.com/showthread.php?t=41360
Whichever you choose, good luck. Be patient with the carb tuning. Few people get it right the first time.