Rob, assuming the top cover goes around the outside of the bottom of the air cleaner box, the cutout in the top cover has to straddle the intake port that sticks out from the bottom part. See yellow oval superimposed on your picture:

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At this point I can't see any way to mess it up unless the top cover can be fitted with its rim inside the bottom part instead of outside it. That is why I'm guessing that the snorkel on the lower part is somehow blocked or obstructed.