It is difficult to "flood" an A4 it has an updraft carburetor. But I think you are on the right track thinking fuel. If the fuel filter really is empty after having run the engine for a while could there be a leak that is allowing it to suck air rather than fuel? Is the seal at the top of the Racor tight? A check of the Moyer Marine site may give you some insight.
Moyer Marine Atomic 4 Engine Rebuilding and Parts
They are likely to know more
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