I always start with the stuff that I last worked on. My KTM usually falls apart somehow in relation to the thing I tried to fix. You say the carbs are synced and that vacuum lines are not an issue. Assuming your carb bowls are clean and the jets aren't stopped up, I would suggest a some fuel restriction. Maybe your Facet is on the way out? You say you changed the fuel filter. Is there any kink in the fuel delivery lines that could restrict flow?
If not a fuel problem, is there an air restriction? How's the air filter?
I will get your symptoms if the carbs are out of sync, or I have an air leak that causes a backfire into the carbs. Seems like you've already excluded these, so . . . dunno. I'm stumped.
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