As far as the prioritization, I think the gist of the book is that putting down "hard-coded" priorities is a bad idea. A lot of productivity books advocate labeling actions with an A for high priority, B for medium, C for low, or putting them into a "priority matrix" with importance vs. urgency...David Allen is arguing AGAINST that.
But the reason he argues against it is because priorities change all the time. C actions can quickly become an A. Four As may pop up all at once, and your former A gets downgraded to a B. What are you to do then?
Priorities are decided AS YOU DO THINGS. That is why this is called a "bottom up" system. Because at any given moment, YOU look at your list of things to do, decide what is your highest priority, and do it. You don't have a predefined all-powerful list that tells you what is important. You already know.
That next-action that is making your heart pound a little bit when you look at it? Do that one first.
Hope that makes sense.