We don't create the TOC by hand... but with MS Word's wizard. It takes no time at all once the headings are tagged.
From what I've heard you say, I think you adhere to the practice that is so often recommended... that is, get your files out of Word as soon as possible, to avoid errors Word can introduce... so I guess I can see why you don't use the Word wizard.
But what I don't understand is how do you get rid of user errors such as extra spaces, extra paragraph returns... extra page breaks, etc, etc...
Do you make the user clean up their Word files before you accept them?