How to Make Admin Changes without Editing the Core

I’ve made changes to the admin-header and admin-footer to brand the backend of my WPMU site and I want to find a way to make those changes using a custom plug-in (I don’t mind writing it myself) so that they won’t get blown away every time I do an upgrade. I’ve got the plug-in started and it already changes the css but I need to know how I can use a custom admin-header and admin-footer. The changes in them are not major but they are beyond css and I’d rather edit the core than use javascript to do search and replace. I can’t find any way to do this like you would with the normal themes; it appears that all of the calls to admin-header are direct, not wrapped in function calls. Any ideas on how I could do this?