If your airfilter was a really bad flow one and you replace it with a hight flow filter yes it will run lean
the filter sometimes is like a choke in some engines
I remenber having a mower that didnt want to run right and swallowed fuel like mad
when removed the filter to clean it was like brand new so i dicided to try it with no filter and it was better than ever until it siezed!
So if you going for a high flow filter make sure you set it up propely
To set it up just get a new plug or clean your old one(SCRAP IT IF IT IS A CHINESE ONE) if it still good start the engine warm it up not reving more than half the way(should only take 2 mins) and then get in a straight line and go as fast as you can, when you get to your maximim speed press the cluch in and stop the engine and let the bike stop slowly. remove the plug when the engine cooled down, you dont want to remove when its warm because it will burn you and you WILL get a stripped plug hole because the aluninium will be really soft when it hot!(dosent happen very often but its better not even take a chance with that cheap quality aluminium)
If the plug is a nice brown/chocolate black it is just fine, if it is grey/white get your needle on the carb. a bit up(so more fuel can get into the engine), but if it is dark black and oilly it is to rich or your oil/fuel ratio is to high
After a few hours of riding get the plug out again and
IS YOUR ENGINE A 2 STROKE OR A 4 STROKE?
I know it sounds boring but it will save you replacing/rebuilding the hole engine because of a stupid mistake
good luck