use List::MoreUtils qw/zip/;

sub emit_frobs {
  my ($a, $b, $c) = @_;
  for (@$a) {
    my @fb = map { sprintf "%.5f", $_ } @{shift @$b};
    my @ec = map { sprintf "%.5e", $_ } @{shift @$c};
    print PLOUT join(' ', $_, zip(@fb, @ec)), "\n";
  }
}

emit_frobs \@energy_bins, \@spec_cps, \@sigma_cps;
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I don't understand the rest of your question, sorry.