So your problems start with Chapter 3.
If you are working in Book Designer, note that it hates short Chapters. So if 'Step 1' is at the beginning of Chapter 3, you will need to add a lot of line breaks and a manual page break, so that the titles are far enough apart.
So,
1. Delete the current ToC. Go to Notes and links and delete all the notes and links.
2. Set all the headings that you want in the ToC as titles. Then use the format/more tranformations/insert all page breaks option to make page breaks immediately above titles.. Then check to see that all the page breaks have actually been inserted. Add any which are missing. If titles are close together then add some line breaks beneath the shortest ones.
3. Then remake the ToC.
4. To make an automatic ToC, set the cursor beneath the book title and select 'insert ToC' in the 'Insert' menu. If it's not correct then use the same menu to delete the ToC and add more spaces and/or line breaks.
5. For a hand-made Toc, follow the instructions in HarryT's BD tutorial.
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