I'd also made something recently to try solve the same problems. ie working with discussions and threads as apposed to the front page. Check it out here: http://christopherdebeer.github.com/hnCommentWatcher/ check it out if you have a chance.
I made a "highlight user's comments" script (https://github.com/polyfractal/HNHighlightUser), it'd be cool if you could incorporate something like that as well. Sometimes I want to quickly identify all the posts by a single person in a thread.
Very nice work :)