Previous discussion on this type of topic was had
here.
I'd experiment with a dummy tournament for this first, but I think if you run the entire event as a Booster Draft, you can get this to work in WER. Your first three rounds are one pod, where cross-pod pairings are allowed, (and you ignore the draft pods from a player-communication perspective) and your final three rounds are another pod, where cross-pod pairings are not allowed. Then you do a Top 8 cut with a bracket based on standings.
Note that I would contact your local WPN rep if you wish this to be sanctioned, so that you know whether they would prefer this multi-format tournament to be run as Casual Constructed or Casual Limited.