This may help
I may have missed the point of the question here, but if you are trying to use your own header & footer it really is easy to do so (so easy in fact i can do it).
Create a seperate template for each (i called mine slant_header.htm & slant_footer.htm) then put them in the main directory. Then on the options section in the admin panel type, type the relevant file names in the sections which pertain to the header and footer...
and there should be light.
Hope this helps, and apologies if i missed the point of your question