It looks like $file = '"'.$file; would be really slow because you are copying the entire file.

Anyway, it looks like you only need one regular expression (and transliteration):

my $file = <$INPUT>;
$file =~ s/(?:(?<=^)|(?<=\t))([^\t\n]*)(?=[\t\n])/"$1"/mg;
$file =~ tr/\t/,/;
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