Whatever method you use, you're teetering on the edge. I would probably prefer taking in smaller chunks and processing them individually rather than trying to hold the entire thing in memory at the same time. Even if while( $_ =~ /\0/g ) { $null++ } keeps you below the mark, if your file grows by some small amount, you'll be back to bumping into the memory limit again.
In other words, none of your methods really address the elephant in the corner, which is that holding the entire data set in memory at once is consuming all your wiggle-room.
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