Having the tags and warnings in your ToC listed per chapter should be sufficient. (BronxWench will let you know definitely on that)
to alter the order, you have two options, both of which you mentioned. Has nothing to do with ToS or CG, but with databases and record numbers in a database, as to how they display in sequence.
There's no reason why you can't edit the contents and titles for the affected chapters, rather than deleting and re-adding in the sequence you want. Personally, I think delete/re-add will probably be easier. Providing there is a chapter remaining when deleting to re-add, you will maintain your hits, rates and reviews.