To the best of my knowledge, what you are trying to do can't be done within mod_perl. This is because mod_perl will restrict access to the underlying os and the IPC::Run will not be allowed to execute. You will need to do it outside of mod_perl.

What you would be better off doing is to run a local daemon (running on localhost for example) that creates the pdf/ps/whatever file. Your mod_perl app would contact the daemon to construct the file. This will reduce the security risk significantly as well as the memory that mod_perl uses doesn't unnecessarily grow. Remember that mod_perl doesn't release the memory back to os.

hope this helps