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My guess is the carbs are not right.
Either not assembled correctly, not completely clean, damaged diaphragms, or jetting/adjustments are way off.
Put the airbox back on when you have the carbs off, and put the stock jets back in. It's never going to be a rocket off the line, but removing the airbox and using pod filters is going to make it flatter everywhere but on the very top.
Another thing it could be is a fuel restriction from junk in the tank, petcock screen, petcock, or inline filter at the carb inlet.
But I'm betting it's the carbs.
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