Overwriting custom_header class

Hi!

I have set up a WordPress with multisite activated. I want my users to use a custom made theme. In the theme, I want the users to be able to select a specific color and upload a header image of any size. The standard custom_header.php does however require a predefined size of the header image, which is not desired in this case. I modified the custom_header.php to work as I want it to be and I’m very satisfied with the result. However, hacking the core functions is not so optimal when it comes to updating a WP installation, since my modifications to the function will be overwritten to its original state when updating.

So, my question is ho to somehow let my theme or whatever overwrite the original file/class/function. The filter function where you add hocks does not seems to work, I guess it’s because the custom_header is a class rather than a function.

cheers,
/L