I don't know what problem you encounter, what is stoping you to do so?
I guess the problem is that the Header-2 headings continue numbering from the previous section.Correct? It looks as if in the definition of Header 2 you unchecked the "Restart numbers at this level" checkbox. If you check that box it should work.
Thanks for the reply to this also.
It must of been a glitch in the styles as I deleted them all started from fresh after what I have currently learned about levels and all seems to be ok. I think it may of been caused by 'duplicating' the styles then editing them. I'll avoid this in the future.
'Header 1 - level 2, and so on' also works okay without introducing a 'Section - level 1' which is what I want as my sectioning is likely to take place after my 'introduction' chapter.
I will have a go at your other suggestion with the script using  for references when I am back at my desk which will probably be tomorrow now.