You Only Live Twice ends on a bit of a cliffhanger which isn't resolved until the next book, The Man with the Golden Gun, but there are two movies between those which have nothing to do with that plot point, so waiting for that resolution is a pisser. Also, there's character development that occurs for the main cast throughout the series, mostly Bond and M, but it gets confusing if you don't read it in order.

Each can stand on its own, but things happen in earlier books that have an affect on later ones, and if you read the later ones first, you're left wondering about stuff like 'why the hell does Felix Leiter have a hook for a hand and why isn't he with the CIA?' You find out in Live and Let Die which is the second book, but that's been spoiled for you if you read Goldfinger, Thunderball, or Diamonds are Forever first, all of which follow Live and Let Die in the book order but precede it in the movie order.

The official project is complete! Reading the novels/stories along with the movies was fun for the sake of comparison, but reading the books in order is definitely the better way to go.