Solved! I used this:
foreach ($query2->result_array() as $row2)
{
//check to see if item is qualified and if yes, then add to qualified, not_qualified, or notApp count
$item=$row2['item'];
$sql3 = "SELECT a.qualified
FROM standard_activities sa, relation r, activity a WHERE sa.activity=? AND sa.id=a.id";
$query3=$this->db->query($sql3, array($item));
}
proof that an old dog can learn new tricks