It seems like the server is quickly getting more bogged down for each day. Have you considered having an admin or something walk around spawn villag and see which areas affect CPU usage in the server the most? That way it might be possible to figure out if there are specific areas that are eating the server or if it's "everywhere". And once that is determined one can look at what exists in that area and see what could possibly be the cause.
Another thing would be to look into how much computer power different things really do use instead of guessing. Like setting up an empty server and filling it in turn with animals, pipes, quarries, running water, dropped items, computers and other things we suspect might affect performance, and then see how much cpu they use in reality.
But I realize this is a lot of work for an admin team that already have their plate full. Though I honestly don't know what to do otherwise? Eventually the server will be on it's knees, so something HAS to be done sooner or later. It would be great if we didn't have to just wipe the server every two months due to it going on its knees.
Edit: found a thread on the issue http://forum.feed-the-beast.com/thre...formance.3536/
Maybe restart the server more often? Every 6 hours or so? Given the short restart time this won't be an issue anyway.