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["Philippe Joyez" <address@hidden>]

In order to achieve what you want you'll need to modify or override the style
definitions. AFAIK such modifications are not directly accessible through
menus and dialog boxes.

For fine-tuning the headers to you need, have a look in the doumentation files

 header-header-dtd.en.tm
customize-layout.en.tm

and try redefining header-primary similar to what is done in customize-
layout.en.tm
to achieve what you want.

For the adjusting the TOC, see std-automatic-toc.en.tm. In that case you can
redefine a blank toc-main-2 (I guess) for the section you do not want to
appear in the TOC. For your layout issue with dots, it will probably require
quite more work, adjusting some macro to do exactly what you want -- look into
the source of the TOC tag (with the wrench icon) and in the style file you
use, to see which one(s) you need to modify. A simpler alternative would be to
define a shorter (or shortened with ellipsis) toc entry so that it remains on
a single line.

If you cannot manage to get what you want in a reasonable amount of time, the
ultimate ugly hack is to directly edit the pdf file itself (with, for
instance, "master pdf editor").

Philippe