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File named "timing.log" is created in current directory, containing the number of seconds each rule took to run, in the 2nd and 3rd columns.
You can also add the loadplugin line to your normal configuration, it might marginally slow down scanning, but should not be noticeable.
More general advice
SA should log per-message scan times to the system log. From that you should be able to determine a message recipient and message-ID for messages that take a long time to scan.
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