1) For those who will be using Word 2000, save your document as a Word 2000 template (not simply a .dot file).
What do you mean with "not simply a .dot-file? I save it as a 97- 2003 template, that is the only .dot format I can see?! Is there any other .dot format?
Under the compatibility options you set it to only use features available in Word 2000. One way of getting to this is File > Options > Advanced.
These are at the very bottom of the dialog box.

2) Themes are intended to allow a person to quickly change the look and feel of a document by changing a theme. Do you want your 2010 users to be able to do this with your template? I think not. To avoid this in the Word 2010 template will require (I think) use of custom styles not based on built-in styles with a formatting restriction to only use those styles. In any case, distributing the theme separately would be a real headache unless you are using installation software.
Well, my only wish is to give them a document with:
a) My paragraph styles and Museo (the font) as the default-font.
If I can make the font-embedding work I think my company-paragraph-styles in combination with setting the standard font will take care of that.
Again, make some custom styles with these fonts. Have your entire template use these styles. In addition, change the fonts in all of the styles to be those that are acceptable to your template and theme.

b) The company selection of preferred colours.
This seems like a bigger problem if I not using the theme-colour witch I can't if Im going to save it as a 97-2003-template.
So HOW do I set the company colour-scheme for them to chose from???
Styles won't do it as far as I can understand?!
I don't know anything about colour palettes. Sorry. Restricting a 2000 template to a particular colour palette is beyond my experience. You can use the character styles like Emphasis, and Strong, as well as the variations on them. This goes against my advice to make custom styles. Emphasize in training how to make color changes by using styles and have character styles that implement what you want. See http://answers.microsoft.com/en-us/o...0-05cc8db807e1

3) The setting for Automatically update styles from template should be turned off (unchecked).
Where can I find this checkbox?
If you start with a document before making it a template, it is on the Developer Tab under the Document Template button. The button is disabled in templates but the setting in the original document carries through to documents made from the template.

Colours are nice. Will all users be using colour printers? Have you discussed this with your customer?
There is hardly any B&W printers left in the offices today and most letters are sent by e-mail or as pdf anyway. The correct colour is an important part of the company's brand in all marketing material and even letters.
The question is HOW do I get the company colour scheme available in the document without using theme-colour?
Again, use character styles to carry your color selections and train users to use them.