I'm about to submit a phd thesis for assessment, but have encountered a strange issue in a couple of chapters.

Basically, the text doesn't follow on as it should within the paragraphs and/or between pages. So the reader will read the paragraph, suddenly encounter huge gaps or blank spaces between text, and then have to skip half a blank page to continue on reading (and potentially encounter the same problem again)

The problem seems to occur when I have a lot of footnotes on the page. But since the thesis literally has thousands of footnotes, and the problem appears to be random, I'm not sure why it might be happening in the first place.

A less urgent issue: I used to able to begin inserting page numbers from any point in the thesis, and would be able to divide my chapters up accordingly.

But now that I've merged all my chapters into a single document, Word is not letting me begin the page numbers from the preferred point (page 9 onwards, when the chapters officially begin). I'd appreciate help in working out this relatively minor issue too.

thanks in advance