For the curious, I'll post what I ended up doing. One of the main requirements of this script was that it carefully preserved the formatting of the files that it ran on- the only change could be the addition of the url markers, so that influenced my solution. the script would be called with two files- one html and one plain text. Sample html file to call with:

this a link: <br> <a href="http://www.somewhere.org/foo">somewhere</a>
+<p> <a href= https://somewhere.else.net/bar/>another place to go</a>.
+<p>
[download]

And sample text file pair to the html file:

this a link: 
http://www.somewhere.org/foo
another place to go:
https://somewhere.else.net/bar/
[download]

so here's my code to tag the urls in these files:

#$unprocessed_html holds the text of the html version of my file
#$unprocessed_text holds the plain text version of my file
#@markers holds the unique url markers, ie [/qfk33pe][/nnd92093]
  
  #handle html version
  my $processed_html = "";
  
  while (length($unprocessed_html) > 0) {
    
    if($unprocessed_html =~ s/^(.*?\b(href|action)\s*=\s*)//si) {
      $processed_html .= $1;
    } else {
      $processed_html .= $unprocessed_html;
      last;
    }
    
    if (not(@markers)){
      $processed_html .= $unprocessed_html;
      warn "no more markers available for remaining links\n";
      last;
    }
    
    if($unprocessed_html =~ s/^([^\"\'][^<>\s]*)//) {
      my $url = $1 . shift(@markers);
      #strip double //s due to sloppy input
      $url =~ s|//|/|g;
      $processed_html .= $url;
      
    } elsif($unprocessed_html =~ s/^([\"\'])([^<>]*?)\1//) {
      my $url =  $1 . $2 . shift(@markers) . $1;
      #strip double //s that can result from sloppy input
      $url =~ s|//|/|g;
      $processed_html .= $url;
    } else {
      die "something happened here";
    }
    
  }
  
  #handle text version  
  my $processed_text = "";
  while (length($unprocessed_text) > 0) {
    
    if($unprocessed_text =~ s/^(.*?\b)http/http/si) {
      $processed_text .= $1;
    } else {
      $processed_text .= $unprocessed_text;
      last;
    }
    
    if (not(@markers)){
      $processed_text .= $unprocessed_text;
      warn "no more markers available for remaining links\n";
      last;
    }
    
    if($unprocessed_text =~ s/(http[\S]+)\s+//){
      my $urlfound = $1 . shift (@markers);
      $urlfound =~ s|//|/|g;
      $processed_text .= "$urlfound\n";
      
    } elsif($unprocessed_text =~ s/(http[\S]+)$//){
      my $urlfound = $1 . shift (@markers);
      $urlfound =~ s|//|/|g;
      $processed_text .= "$urlfound\n";
    }
    
  }
[download]

-- cat