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If you run the script which focuses on the flagged projects, you can go to the sidebar after the script runs, select all the flagged projects, copy them and paste them into a document (TextEdit and OmniOutliner are apps which will work). You can then reorder the rows of the document as you like to generate your prioritized list. The rows also serve as hyperlinks to OmniFocus, so when you want to work on the first project in the list, just click on it and you'll be transferred to OmniFocus, where a new window focusing on that project only will appear.

This approach is not limited to projects; anything you select in OmniFocus and copy/paste in this fashion should work. So, if you need a prioritized list of actions, you can do that as well, though you'll need to build up the list separately for actions and projects.