Small correction:
SetLogLevel changes take effect immediately -- as do those made via the corresponding HTML UI, Windchill/wtcore/jsp/jmx/logLevel.jsp.
Changes made to the settings by editing the log4j*.properties files will take effect in a matter of minutes (3 or less).
All that said, exception stack traces are mostly associated with ERROR (or FATAL) log events -- and these are logged by default without having to change any log levels.