a) b) Do it like C programmers do... use a preprocessor :) Join all these lines into one big happy line. Save output to a new file and work with that.

Like that (very briefly tested, seems to work):

use strict;
use warnings;
use feature 'say';

my $headers = qr{
    \A
    \s*
    (?: LOCUS | DEFINITION | ACCESSION | VERSION | KEYWORDS | SOURCE |
+ ORGANISM | CDS )
}x;

my $skip = qr{
    \A
    \s*
    (?: Data\s+file: | \/\/ | \z )
}x;

my @lines;

while (<>) {
    next if /$skip/;
    s/\R//;

    if (/$headers/ and @lines) {
        say @lines;
        @lines = ();
    }

    push @lines, $_;
}

say @lines if @lines;
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