My interaction with Apple goes via Smashwords, I have had no difficulty resubmitting books through them, nor through Amazon. It is not something I make a habit of. I have never had a book rejected due to advertising problems, but I doubt if they treat it much differently to any other issues (unacceptable cover sizes and so on).
Judging from my own experience, and what I see in other books, no one is going to complain if you make it obvious that the book is part of a series and provide information relevant to the rest of the series - providing such information does not advertise reseller competitors. Linking to your own website does not seem to be a problem, and you can do what you want on your own website. If you were to create separate editions for each reseller, I imagine you could probably get away with inserting relevant links back to that reseller, but it's not something I have ever bothered with (but I am very lazy with regard to marketing).
As a reader, I would look on any request from the author for "tips for improving the book" with an unkind eye. Such a request smacks of amateurism. I buy a book with presumption that the author has already done everything they can to produce a finished product, it is not my job to help the author fix it. (Note: technical and educational material is a bit different in this regard.)
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