I will answer any burning questions about the Twitter API. Issues you might be having, OAuth, rate limiting, you name it I can probably answer it.
What makes me qualified to answer Twitter API questions? I am the all time top poster on the developer group: http://groups.google.com/group/twitter-development-talk/about and my TwitterOAuth library is the 4th most watched PHP repo on GitHub: https://github.com/languages/PHP
Edit: Feel free to contact me through other means as well: the@abrah.am or @abraham
The ugly way a coworker and I ended up using was to just see if the single tweet was in response to an ID, request that ID, see if that was in response to an ID, and so on until it either ended or we cut it off prematurely after a certain conversation length. This method also doesn't allow you to see any future messages within that conversation.