Very insightful post.
I have worked through a lot of projects like you describe. Some of them were kind of Agile. I always got beat up after my estimates turned out to have been too optimistic.
The best standups in my experience were short and everyone was encouraged to say a little bit about what they were doing and definitely to ask for help if they ran into a tough spot.
I never got much out of the weekly retrospectives we had to endure.