I think you want to get rid of the backslash and let the variable be interpolated in the double quotes. Change:

        $htmlFiles.= "\$lists[$y] ";
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to:

        $htmlFiles.= "$lists[$y] ";
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You could also simplify and use the array directly because it'll interpolate and add spaces for you ($"):

my $result = `wkhtmltopdf.exe @lists $project.pdf`;
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