The second issue is headers and footers. HTML and Excel don't have them, but PDF does.

As per my earlier post -- you can utilize the proposed W3 extensions for this. For example, see this fragment taken from CSS Print to put a running page count at the bottom of pages:

<style>
 @page {
  counter-increment: pages;
  @bottom-center {
      font-family: Times, Palatino, serif; 
      font-size: 12pt;
      font-weight: normal;
      content: "Page " counter(pages);
  }
 }
</style>
[download]

Sure, a lot of these standards are proposed/preliminary, but I think they offer a good place to start because a group of people have already been thinking about these sorts of challenges.