So we're back and seemingly safe. We've got most of the other subsites converted over, but we've found after relaunching the main MetaFilter site and Ask MetaFilter, the server now has some serious uptime issues.
We're going through the possibilities now, but I wouldn't be surprised if the added overhead from extra security on all queries is causing the slowdowns. The server is zippy when it's online though, but it is dying every 20 minutes or so.
One possible path is to move to a new hardware setup, but that will unfortunately take a couple days more to accomplish.
Hopefully things will be back to normal in a couple days after some more tinkering, but things will be rocky for the rest of the weekend.