Double check all vacuum caps. You mention two lines, but there are four vacuum ports on the manifolds. If you use an air flow meter to check carb sync, you can remove all lines and seal the four ports. It removes one possible source of problems. Also, carbs way out of sync will do just what you describe. I don't know why they would jump out of sync, but when my bike goes a little out of sync, it pops just like that.
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