I've never seriously kept a thought diary. I've kept a "thought dump" but I might try to write down more thoughtful notes and later try to go over them more critically.
I especially like your idea of keeping regular contact with management about delays. It reminded me that I've actually done that a couple of times and it really felt liberating. Like... taking actual responsibility and not hiding it, but at the same time... somehow sharing the responsibility because you obviously can't handle the task at hand alone.