So your "application" is "timing server side performance for a CGI script". If you are interested in perceived slowness by a real user then any time period less than 1/2 a second is uninteresting. Trying to measure times with 1 ms resolution in that context is neither meaningful nor useful.

Wall clock time for the server process is the only thing of interest to a "someone" at the far end of the pipe and that can be obtained using Time::HiRes::gettimeofday. If you determine that there is a performance issue on the server then you have the harder task of determining where the bottle neck is.