If you have the qlikview desktop installed/licensed on the server, you could run a morning batch file and bypass the Publisher all together:
"C:\Program files\Qlikview\QV.exe" /r "\\<server>\<drive>$\<location of .qvw>"
Maybe try 10 at a time at first and gradually increase. Maybe you could get to the 100 mark.
It will run as many concurrently as your "Max Concurrent Reloads". The remainder will be queued "waiting for engine". If a task does not get an engine in the proscribed timeout (default 45 mins) it will fail. To modify the wait-for-engine timeout, update the value for "QvbWaitTimeoutMinutes" in
"C:\Program Files\QlikView\Distribution Service\QVDistributionService.exe.config"