Ran into similar performance issues with some of clients PHP applications. However using APC and memcached solved most of them. Add some properly configured mod_expires to your apache and switch of php's ultra-stupid autosending of headers.
You might also think about setting up a server for static contents, thttpd or lighttpd will give amazing results about throughput and take away the work from your apache.
Another thing that really provides great hints for optimizing is xdebug together with wincachegrind (or kcachegrind), it will s... (
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