Please excuse me again, but I have been playing with a similar 'problem', so
appreciate any feedback you may have...

Consider that when following an anchor link (or a link that opens in the same
browser window) that 'focus' changes.

Alternately, a "footnote link" could open in a new browser window,  Focus in
the primary document remains unchanged.  To return to the same spot, just
close the new window.  This should be true in most browser 'flavors'
(excepting those that are configured to disable new windows, etc.)

I found an example that uses D links @  <A
HREF="http://www.ncddr.org/du/products/bp.html">
http://www.ncddr.org/du/products/bp.html.</A>  What I like is that all the
'footnotes' could be contained within a single page, and therefore be read as
a 'unit', or one at a time from the primary document.  It is also possible
have both documents open, and read from either one (using Alt+Tab to move
between them) without affecting focus in the other.  The link that closes the
new window is probably a javascript, but couldn't the window also be closed
using the DOM?

I'm thinking something like this might be a solution.  What do you think? And
hey...there's probably still a place for an accesskey in there somewhere!  (I
just love accesskeys, don't you?)

Sorry if this got a bit lengthy, I can tolerate a gentle scolding if
necessary :)

Marlys