You could try to play with $includeHeader variable defined in setup_options.php. Create different PHP headers for your forums and in bb_plugins.php then define:
if($forum==1) $includeHeader='header1.php
';
elseif($forum==2) $includeHeader='header2.php';
....
else $includeHeader='header_main.php';
Please note than for custom PHP headers you need to define all miniBB variables as globals. For example instead of {$title} you need to define:
<?php echo $GLOBALS['title']; ?>
etc. with all possible miniBB vars.
I am not sure it will work so the solution is in your hands. If it will work, report here please, so I could move this topic to "Custom modifications" forum.