Please tell me how I can test:

- Why that 404 error appears

- Why sometimes it takes so long to display the same kind of page other
times displays much faster

- How can I test where the script hangs, which part of the script is so slow

I'd look into your apache error logs

you can also do a

     print STDERR "crap"

on certain blocks of  code and
    tail -f /var/log/apache/mp_errorlog
(thats my error log for  modperl)

then look to see where stuff is hanging

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