There are probably a number of permission problems but I believe the first problem is that the wwqmt directory expects to be outside the moodle directory structure. The setup.pl script copies files from the .../wwqmt directory to the /var/www/moodle/question/... directory. The directories that you enter to the script.pl routine are the location of wwqmt (e.g. /tmp/wwqmt) and the top level of moodle (/var/www/moodle).
In addition the wwqmt (webwork question type) is not really a module and will not be included in the moodle/mod directory (the wwassignment webwork-moodle bridge on the other hand is a module). The wwqmt webwork-moodle bridge extends the question types defined for moodles quiz module.
You still need to enter the url for the WSDL even if it is on the same machine running moodle.
Hope this helps.
Installation
Installation Problem on CentOS 5.3
This forum has a limit to the number of forum postings you can make in a given time period - this is currently set at 5 posting(s) in 1 day