I found that the monobook skin relies too much on
absolute positioning
to make even minor mods easy. I completely re-jigged monobook.php to
use relative positioning by just rearranging the order of the various
<div>s on the page. That way, changing one <div> automatically bumps
the adjacent <div>s.
Sounds interesting!
Is your wiki publicly accessible, and could you share those modifications?
-- F.