Can I reference brand names and the names of chain stores in my novel?

Yes, as long as you don't give the impression that the brand owner endorses or approves of your book, or that you're trying to trade on their good reputation. It might be advisable to avoid saying negative things about the brand, but I've never heard of a writer of fiction getting into any sort of trouble for that.

The only case I'm aware of where a novelist got into trouble for using trademarks was someone who published a book with a cover that looked a lot like the label on a bottle of Jack Daniels. A reader might reasonably believe the book was an official Jack Daniels product, or that the company given permission for the author to use a design similar to theirs. It wasn't, and they hadn't, so the author had to change it.

Yes - within limits. If you have a murder in a McDonald's, you can't have a Mickey-D's employee be the killer, and you can't have McD employees being inept or cowardly, and you can't have McD management to cover it up, etc. In other words, the murder can happen in a McD's, but it can't make the brand look bad.

*facepalm*

How much do you read? If you read often you would already know the answer to this.

Yes.