An alternate approach is to "pipeline" the process. Split the stream into tokens, operate on the tokens, and then reassemble the tokens. This might be overkill for your particular example, but is still a useful technique to have in your bag.

  my $string = "|90|93|foo|bar|91|92|95|96|906|";

  my $result = join "",
               map { s/^9[0-6]$/X/; $_ }
               $string =~ m/(\||[^|]+)/g;

  print $result;
  __END__
  |X|X|foo|bar|X|X|X|X|906|
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It's tempting to use

  split /\|/ $string
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to do the tokenizing, then

  join "|"
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to reassemble them, but you'll lose the trailing "|".