Having the stock air filter setup connected and sealed properly allows the carb to get the correct a/f ratio. If you allow more air in, it throws the mix off. Most bikes, atv's, and utv's are the same. Guys like to get a new ride and take the filter lid off without rejetting, same issue, it will run like crap. Tiny changes in fuel and air will throw these little carbs off. In a 350 Chevy, it's a little different story, most of them are over fueled lol.
Sounds like you got it fixed.