James:
I suggest that you create "Next:" and "Previous:" links between each of the subtopic pages in the Guide topics. You've done it in some places, but not all. The quantity of links on each page is great, but to get a complete picture of the program, the user is now required to page back to the start page in order to move forward to the next subtopic.
I continue to think about your stated goals for the help files (as mentioned in the discussion about my confusion about the Rolling Merge, you'd like to keep them short and succinct) and I believe that with software of this depth and complexity (despite its surface simplicity) you might seriously consider a more thorough manual in a different form -- say as a PDF or RTF, etc., attachment. (Or I could propose to David Pogue a QRecall: The Missing Manual
.) I think you need more space for examples and analogy.
Best,
Steve