So the forum's been running on MyISAM the whole time?
Boy, does that explain a few things.
No it has not, most of the database was on InnoDB but a few of the tables contained text columns that were preventing them from being moved across to InnoDB due to the lack of full text search. The issue was the background maintenance tasks were performing a join with one of these tables, which would then cause a lock contention and stop general forum use. That lock would cause a massive backlog of traffic and a huge spike in CPU load, etc... It has involved a ton of testing to determine where the fault was before throwing "fixes" at the server.
When you have a website that is as busy as this and no dev/test platform, you can't just to haphazardly upgrading packages, until now the remaining two MyISAM tables have not been causing an issue, but as load has gone up on the website it became a problem.
There are a few things that are planned to improve website performance, the server is in need of some TLC when it comes to new/faster technologies, etc, it has just had to wait until I could ensure I had enough time to perform the changes and deal with any new problems that may arise. The up side is we get a faster website, the down side is there will be outages in order to perform this work.