Code lifted from the POD in File::Find::Rule and HTML::TokeParser::Simple and adapted. Not tested, so proceed with necessary caution, though I don't see any mistakes.

#!/usr/bin/perl -w
use strict;

use File::Find::Rule;
use HTML::TokeParser::Simple;

print "Processing:\n";

for my $file (File::Find::Rule->file->name('*.shtml')->in(@ARGV)) {
    print "\t$file,\n";

    rename $file, "$file.old" or die "Cannot rename $file to $file.old
+: $!";
    open my $fh, ">", $file or die "Cannot open $file for writing: $!"
+;

    my $p = HTML::TokeParser::Simple->new("$file.old");
    while (my $token = $p->get_token) {
        print $fh +(
           $token->is_start_tag('a') ?
               new_a_tag($token->return_attr, $token->return_attrseq)
               : $token->as_is
        );
    }
    close $fh;
}

print "done.\n";

sub new_a_tag {
    my ($attr, $attrseq) = @_;
    $attr->{href} =~ s</main\.php\?page=!></?id=!> if exists $attr->{h
+ref};
    map "<a $_>", join ' ', map qq<$_="$attr->{ $_ }">, @$attrseq;
}
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Update: fixed some small left-overs from the POD version of the tokeparser code.

Makeshifts last the longest.