Yes, we basically agree. I agree that the book needs to be read several times. When I finally signed up to the Barnes & Noble Course, just to get a different view of the same material, there it was in black and white - the 5 stages are separate. Only then did it hit me that getting from Inbox to Organized was not the real objective - Processing the Inbox to establish good Organized lists is the way to go. That's why I objected to the hypothesis of combined Processing and Organizing. If my experience is of any value to GtD beginners, it's the costly learning experience that it is a seductive objective to keep the Inbox empty, but if the result is that the lists are no more than a re-shuffled Inbox (categorized but still not Doable), you have taken a step backwards because now you think you are Organized but you haven't really progressed towards Doing. Basically you have put everything back in "In" - it's just a different form of "In".
With respect to electronic lists vs. paper lists vs. pending files, I am sure that few people would disagree that electronic lists are the most manageable. The only problem with electronic lists is that they tempt you to perform unneccessary, time-wasting analysis, simply because the features are there and are easy to use, and to focus on refining the elegance of the system instead of moving along towards the end of the 5 Stages.
I am flattered that you think that I have mastered the concepts. However, I have far from mastered the process To borrow from another thread, I still need to work on Hyrum Smith's character and discipline concepts.