Thank you Tim and Richard. With your help I was able to figure out how to
get this script working as I intended.
Here's the code, in case anyone wants to do something similar in the future.
:-))

$pages=mysql_query("SELECT CP.page_id, pagename FROM cluster_pagetbl as CP,
pagetbl WHERE 
CP.cluster_id = '$id' AND CP.page_id=pagetbl.page_id order by page_id");

$pgids= array();

if (mysql_Numrows($pages)>0) {

        $prows=mysql_NumRows($pages);
        $i=0;
        while ($i<$prows){
 
//figure out how to get page ids into array
$pid= mysql_result($pages,$i, page_id);
$pagename =mysql_result($pages, $i, pagename);
 
 $pgids[$pid] = $pagename;

$i++;
}
}

//prints what is in the pgid array. 
foreach($pgids as $pid => $pagename){
 print $pid.' => '.$pagename.'<br>';
}

$query2=mysql_query("select page_id, pagename FROM 
pagetbl order by page_id");

$mpgids= array();

if (mysql_Numrows($query2)>0) {

        $numrows=mysql_NumRows($query2);
        $x=0;
        while ($x<$numrows){
                
$mpid=mysql_result($query2,$x, page_id);
$mpagename=mysql_result($query2,$x, pagename);

$mpgids[$mpid] = $mpagename;   
  
$x++;
}
}

//prints the checkboxes, compares pgids and mgids array
foreach ($mpgids as $mpid => $mpagename){
print '<input type=checkbox name=page_ids[] value="'.$mpid.'"';
if ($pgids[$mpid] == $mpgids[$mpid]){   print " checked"; }
print '>'.$mpagename;
}

//double check to see what values are in both arrays, then print it.
$diff = array_intersect($mpgids,$pgids);

foreach ($diff as $element){
print '<p>'.$element.'<br>';}

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