Man I hate the let’s remove the airbox crowd. Try to find out what jets were std with it. Maybe he put large ones in to compensate for when it didn’t run properly with the box removed.
Try here , maybe it will list sizes if you can find your bike. Might not have the list for a 400 as US site though?
Start with the obvious first. Take the carbs apart, clean out the jets (never poke anything down them, only blow). Check if needles are in middle position which is probably std if they are adjustable. Check the rubbers are not perished.
New plugs. Check the coils & plug caps are ok, try swap from donor bike. Is charging system ok? This can cause a breakdown.
Best guess is the carbs though. Maybe the donor bike carbs might be a good starting point once cleaned. The 4-1 will make an effect but shouldn’t be as bad as you describe & likely curable with a slight jetting change.
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