Most of the time high cpu usage is wrong or missing indexes.
Best bet is to check the tables in question to make sure has indexes
Without knowing your exact query causing the lag its hard to say what your indexes should be.
Also I would try changing well used tables or really large tables from MyISAM to InnoDB because InnoDB dont lock the table in slow querys.
Ones I would do without looking at the db is users,torrents,files,comments,
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