By rewind he means seek FILE, 0, 0, so that the next read is at the beginning of the file.

And by reverse the loops, he means change:

foreach $term (@inputs) {
  while (<FILE>) {
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to

while (<FILE>) {
  foreach $term (@inputs) {
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I'm going to add a few unrelated points:
Always:

use warnings;
use strict;
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In fact, you probably have a bug of "filenumbers2" vs. "numbers2" that use strict would catch.

Instead of

  push @before, split(' ', $`);
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you should have

  @before = split(' ', $`);
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Then you don't need the awkward @before = undef; The same holds for @after, too.

Really it should be

my @before = split /\s+/, $`;
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The three lines

@before = reverse(@before);
@before = splice(@before, 0, 7);
@before = reverse(@before);
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are better written as splice(@before, 0, -7);. And this code:

  if(exists $results{$number}) {
  $existing = $results{$number}; 
  $results{$number} = $existing . "... @before" . "<b>$&</b>" . "@afte
+r ...";
  } else {
  $results{$number} = "... @before" . "<b>$&</b>" . "@after ";
  }
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can be written as

$results{$number} .= "... @before" . "<b>$&</b>" . "@after ";
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