It may help to combine the non-anchored regexes with one alternation:

s/\:000[A,P]M|99991231|Jan 1 1900 12:00:00//g;
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If, before the while loop, you computed

my @input_field_indexes = map($_-1, @PROC_FIELDS);
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then your for loop could be written

for my $field (@INPUT_FIELDS[ @input_field_indexes ]) {
  $field = '' if $field =~ /SUN/;
}
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And you'd eliminated a lot of repetitive calculations, since @PROC_FIELDS doesn't change inside the while.