Sometimes you find intermediate solutions that you think are fixing the problem, but actually aren't. My previous two posts on optimizing mysql tables, and modifying drupal's path handling, were not, as it turns out, actually the problem.
Well, my previously hopeful mysql optimization routine is not as ideal as I had thought. I've found I have to optimize the table several times a day in order to keep the site humming, and that's not a good solution.
Sometimes you forget the small things... For example, recently at work we switched our website over to Drupal (which powers this site too) and after a few days I noticed it hanging on occasion, for 1-2 minutes. I check the mysql slow query log I have set up, and found that a certain query was taking 1-2 minutes to execute. YOWSA! I dug in and found that the query was called to delete the cache of the menu structure every time the menu *may* have changed, which happens when you update some settings or edit/create a new page. And I checked the database file on the disk and it measured in at a whopping 2.1 Gigs.