I like your header idea. I did the same thing only with CSS. Does your plugin load all the headers regardless of what size is displayed and then only show the correct one? I am finding it hard to position the logo where you want it also.
That testing tool is helpfull too, it is showing correctly the issue I am having so hopefully i can fix it. Myabe I will try the plug in also.
The Footers are a problem too. Very hard to get it looking right.