bike running funny and sputtering/lack of power?

Look inside of the carbs when the bike is running,those black slides should be fluttering back and forth and when you twist the throttle those should lift up quickly and stay there until you twist the throttle back in the other direction.If they are not doing that then the needle attached to the diaphragm will not rise to allow more gas into the system.The slides become dirty with crap and will not operate correctly which is important for quick acceleration.Diaphragms may have a crack or hole and are not working-but when you removed the airbox you removed a bigger size hose that was attached to the carbs and channeled "flow air" from moving into the carbs to aid in the opening of the diaphragms.Check the diaphragms for cracks or leaks,leave the jets alone.

What size engine – unless it is the 500 it is almost the worst thing you could have done.

There is almost nothing you can do to get really smooth running on a GS engine once you have taken the airbox off.

The worst thing you could have done is damage the the airbox removing it – they are difficult to replace.

A good dyno technician with plenty of time could sort it for you to run without – you have almost no chance trying to do it in your garage at home.

Even the GS500 will be unhappy without the airbox but all of the 4s really, really hate being without it.

I had a GS1000 for a while, I rode it once without the air-box and the difference was staggering, if you want to spend money on it you could take it to the bike shop and get it sorted, if not it would be simpler, and cheaper, to just put the air-box back on.