To clean up your document, the first couple of steps are:
1. Make sure you are not tracking revisions
2. Remove any section breaks. I do this with a find and replace but you can do it manually if you wish.
The grey areas you talk about are most likely headers or footers so step 2 may have solved that problem. If the grey returns remain then they could be simply formatted with a colour. You can remove empty paragraphs by find/replacing ^p^p with ^p but you will need to do this multiple times if there are large blocks of empty paragraphs since you are halving the count each time with that replacement.

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Andrew Lockton
Chrysalis Design, Melbourne Australia