Alright, so I want to have the portal page set up so it reads from lets say {$header1} instead of {$header} and {$header1} links to a custom template, iis there anyway to do this?
You need to go into portal.php and define $header1 as whatever you want.
I can't find any sort of {$header}, header, head, etc. in portal.php at all...
I believe it's only located in global.php.
Look at/around line 500 for the header eval'ing.
create a plugin that hooks global_end and then changes the $header value to the value that would otherwise been in $header1.