Oh, OK, if you're using a plugin on hook location parse_templates like we were talking about, then you don't need to render the footer template because that will be done by the vbulletin code. All you need to do is call vB_Template:

reRegister() for any new variables you want to use in the footer template, like:
Code:
// put code here to calculate new variables, then...
$templatevalues = array('activemembers' => $activemembers,
'activeusers' => $activeusers,
'newuserinfo' => $newuserinfo,
'numberguest' => $numberguest,
'numbermembers' => $numbermembers,
'numberregistered' => $numberregistered,
'totalonline' => $totalonline,
'totalposts' => $totalposts,
'totalthreads' => $totalthreads);
vB_Tempate::preRegister('footer', $templatevalues);
Then you can use those variables in the footer template. Your plugin only needs to include the code for variables you want to add, so you don't need ot worry about all the other things in the footer template.
Another way to do it might be to create a small template for the stats you want to add to the footer, render it like you've done above except instead of calling print_output, save it to a string variable. Then preRegister that variable to the footer template, and you only have to insert one variable in the footer template.
BTW, the reason you are getting only the footer showing is that print_output exits the script when it's done, so it can really only be called as the last thing on a page.