The simple answer is to put the stock airbox back on.
You probably need one size smaller pilot jet, and a needle adjustment - and will need to reprofile the needles a bit to get really good performance with pods.
You have to approach carb tuning methodically. Have all internals sparkling clean, especially the main jet emulsion tubes. Do some WOT plug chops to determine how the main jet is doing, adjust main jet sizes to get tan/brown pugs at WOT. Then move to about half throttle and raise/lower the needles to get good plug color there. Finally work in low throttle - you can first change the pilot jet to get that looking good. Lastly adjust the airscrews for max rpm at idle. This will leave you with some flat spots and surging, pods are not so easy to tune for.
To properly tune the carbs for pods you next mark the throttle grip at ~1/8 travel intervals and do plug chops to see if any are too rich: adjust the needle heights until some are lean and some are good but none are rich: record the throttle settings and the result ie good, bit lean, very lean. You then set the throttle to a "lean" position and mark each needle where it enters its main jet, remove it, and chuck it in a drill or drill press. With a cloth and brasso/solvol pinch each at the marked point while it's turning, to thin the needle a bit (and richen the mixture). Then repeat the plug chop until that spot is correct ... and move to the next lean setting. Of course you can only make the needle smaller, so don't overdo it.
If that gets you good plug color at all throttle settings and you still have surging or flat spots at low throttle... the slide cutout probably has to be changed. Not easy. You can increase it (with difficulty) but reducing it is not practical.
This takes a LOT of iterations and is a super PITA. Putting the OEM airbox and filter back on is much easier.