I would suggest posting over in the Server Configuration forum on vbulleitn.com. George would probably have some advice on what you can change setting wise to help your server.
As for cleaning stuff out, you can prune logs in the admicnp > stats & logs but I doubt that is going to change much on the site. I assume you already have all attachments/avatars/etc in the filesystem, not the database. You can prune users that haven't visited in x amount of time or threads that haven't been posted in for x amount of time.
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