Indeed I have tweaked the numbering manually, in a desparate attempt to make the target Hebrew numbering match the original English style.
Seems I'll have to go through this in the proper Word way (i.e. losing half-a-night sleep).
Not necessarily - what you'll need to do is to properly define the styles for Heading1/Heading2/Heading3, and apply it to the relevant section headings.
What did you mean by "use the cleanup macro (TW4WinClean.Main)"?
The Trados template includes a macro called tw4winClean.Main, which will remove source text from your document (=clean it up). The difference between the macro and the Cleanup task is that (i) no backup file will be created; and (ii) your TM will not be updated with any subsequent changes made during editing. Therefore, the macro should be used with care, but can be extremely handy if there is a problem cleaning up.