It really shouldn't be the filters but as another member mentioned make sure they are not in too far. It could be coincidental that you are getting more flow and are now misfiring.
Are your spark plugs original? That is likely the culprit 9/10 times.
They should be changed every 20-25, if you are tuned.
It may be behoove you to ensure the filters are on straight, if you can't access it correctly, you should remove the cowl, it's about 8-10 8mm bolts.