Stopping the message board and reopening it cleared up the server issues--I don't know why. I will keep monitoring it and see if I can get a better handle on the situation, but I do have a theory that it might have been related to resetting some counters in the DB (part of the vBulletin 4 upgrade process that has to be manually initiated by an admin). I'd be curious if folks are still noticing slowdowns because the server load looks pretty reasonable right now. (There are a few things I plan to do to mitigate performance issues a bit more, like moving all the CSS back to the file system, but I don't want to do that until I've fixed the layout issues since those changes will start getting cached by the CDN and browsers.)
The positioning of content in posts containing ads should now be fixed.
I made most of the smilies pretty (except because it had no equivalent).
FYI, I found a few settings around marking threads read. The current settings are basically "fast and inaccurate"; there are two other settings that involve more DB hits that are apparently more accurate. I don't want to change this right now because I'm seeing unusually high server loads at times, so I want to avoid pushing it further at this time.
Regarding the "hot threads" -- I don't see this issue. It looks like any thread with 15+ replies is currently getting the hot icon. Can you point me to the specific threads you're noticing?