I have almost exactly the same problem. I hope someone can help here.
You can see the symptom by going to my site: https://www.shilsholecommunity.org. Most posts older that April 1 show the “question marks” in place of special characters.
I got to this state by doing a backup (exporting) from an old MySQL DB (3.23.58), and importing into a more recent MySQL DB (5.0.24a). I then changed the wp-config.php setting to point to the new DB, but I didn’t change the wordpress code at all. I did this to prepare to upgrade from WP 2.0.2 to 2.1.2, since the upgrade requires MySQL v 4.0 or later.
Thanks!
