Luke, Alex: After reading through most of Eliezer's 2006-2009 posts over the last 3 days, I suggest including in the eBook all the out-of-sequence articles you listed, except:

• The Cartoon Guide to Löb's Theorem
• Conjunction Fallacy (summarized adequately in lots of other articles, especially Burdensome details)
• Cynical About Cynicism
• Fake Fake Utility Functions
• For The People Who Are Still Alive
• Locate the hypothesis
• The Martial Art of Rationality
• The Modesty Argument
• No One Knows What Science Doesn't Know
• Optimization
• Passing the Recursive Buck
• Possibility and Could-ness
• Priors as Mathematical Objects
• Rational evidence
• Rationality is Systematized Winning (don't need a whole article for this; to the extent it isn't just a recap of the Newcomb's Problem article, the point can be made in one sentence in the Introduction, or in a slightly edited What do I mean by rationality? and/or Incremental progress and the valley)
• Surface Analogies and Deep Causes
• The Two-Party Swindle (interesting but not essential, and copy-pastes content from other pages)
• The Ultimate Source
• The Unfinished Mystery of the Shangri-La Diet (this and Akrasia and Shangri-La are both too specific to be good core sequence candidates; their message is better covered in Beware of other-optimizing)
• We Don't Really Want Your Participation
• Why is the Future So Absurd? (use Stranger than history instead; showing is more powerful than telling)
• You Only Live Twice (already in the FOOM eBook)
• Zen and the Art of Rationality

From what I can tell, all the links to those pages within the Sequences are minor passing mentions, and their contents aren't particularly valuable for understanding the core content of the Sequences. Understanding Free Will, for instance, isn't needed for the rest of the Sequences, and EY actively discourages just copy-pasting his answer here.

I note that about 25 of the posts from the Quantum Mechanics / Timeless Physics sequence also aren't necessary for understanding the rest of the Sequences, differ in tone in interesting ways (they remind me of 2010-2013 Eliezer), and make the QM section look a heck of a lot more intimidating than it needs to. They also need new images to replace the quick pencil drawings, so I suggest leaving out the more technical stuff and then consolidating all the QM posts in a future eBook, once the images are polished up.

I can also suggest places to integrate the new additions that will make it possible to read the entire Sequences eBook from front to back without doing any hopping around. It doesn't take very much reshuffling to make the dependencies work sequentially in the Sequences.