Markus Büchele wrote:
Hi Lyx experts,

I have been using LYX for over decade now. It has always been a fantastic tool, especially for my PhD thesis. Unfortunately I have arrived at a dead end just before publication. My publisher (Franz Steiner Verlag, Stuttgart, Germany) has very percise ideas about the layout of the text and I am unable to adjust to his wishes with LYX.

All of this can be done, probably without too much trouble.

Things which need to be adapted are:
* font in the header, which has to be small capitals instead of capitals and a different font size

I assume here that you mean the page header, or do you mean the chapter titles? Adjusting the page headers can be done use the fancyhdr package, and is fairly simple.
   http://www.ctan.org/tex-archive/help/Catalogue/entries/fancyhdr.html
Adjusting the chapter titles can be done using the titlesec package and is also fairly simple.
   http://www.ctan.org/tex-archive/macros/latex/contrib/titlesec/
We can work out the details.

* header (left pages): the word chapter is printed in all chapters in German ("Kapitel" which is correct), but in chapter 9 there is "chapter" in the header (a bug?)

Did you have some English in the document somewhere? It seems as if the language has gotten changed.

* space of indentation at the beginning of paragraphs

In your preamble, put:
   \setlength\parindent{2cm}
or whatever it is you need. LaTeX will accept lots of different units, too. See here: http://www-h.eng.cam.ac.uk/help/tpl/textprocessing/teTeX/latex/latex2e-html/ltx-86.html
for help.

* headlines of chapters without the word "chapter" in the headline and different font size

I think this is where you want to use titlesec.

An alternative might be to switch to use the book (koma-script) class. The koma-script classes provide for a LOT of customization.

Richard

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