I would try removing (or commenting out if you prefer) the $* = 1 line and add the /m modifier to the match inside the last while. That's only a guess but it would make sense for the . not to match the newline here, I think.
while (/(^|(\r?\n))[^0-9]*((\d\d\d).*)$/mg) {
Back your script up before making any changes, of course.
How long have you had that script? It is in quite an old style.
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