if you really want to optimize mysql, you have to recompile it aside from tweaking the config file. here's a link regarding mysql optimizations:
http://www.devshed.com/Server_Side/MySQL/Optimize/page1.html
you also have to optimize the client queries.
btw, it this intentional? set-variable = wait_timeout=2880000000000
if the problem persists, consider adding an additional memory or applying a load balancing technique, etc.....
HTH
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