See what size main and idle jet are in there now. With a stock airbox, filter, headers and mufflers the jets should be #75 main and #40 idle. Most people install a larger main jet (#80 or larger) and drop down to a #38 on the idle with pods installed. Often the needle clip is changed with pods, so you will need to put or confirm the needle clip in the middle position for use with stock confirguration.
I have built several CB400F's with both stock and pods filters and have learned one extremely important detail, use only HONDA OEM carb parts. The quality control and materials of the aftermarket carb kits are poor and cause all kinds of problems when tuning your carbs. Very frustrating and time consuming. Do it right the first time. Good luck and post your results.