Not exactly a match made in heaven... I spent the better part of this evening attempting to upgrade to MovableType 3.14 and MySql 4.1.8. Things went well until I actually tried getting the web site back up... It turns out that the latest MovableType doesn't know how to talk to the new MySQL properly, the password encryption changed with 4.1.x, and so I was never able to log in properly.
I spent the evening searching for some official workaround, an update to some code, etc. The best I was able to find was a hack that told MySQL to use the old password scheme, which looked like it would have resolved the problem, but I decided to get the site back up and work on it more later.