Scroll up for the longer existing discussion I’ve merged your query into, but one quick tip I do not see pointed out much (or at all) is that special-purpose compile Formats often come with a “Table of Contents” Section Layout that is already set up to handle the formatting for you, based on the size of the paper it is intended for.
That aside, if you do end up going the route of using Word to clean things up, I would highly recommend doing that the right way rather than trying to get good results from this tool. A proper ToC inserted into Word, when coupled with properly styled headings, will update dynamically when headings are revised or sections are added/moved around. Plus it should be more efficient once you have it set up, as it is just one command to insert a ToC in Word instead of a bunch of line by line cleanup (particularly with section/subsection level indented contents).