I, as a PnF fan, got interested in this search as much as the OP and did my own. I was able to find one of the two lost episodes(the one that isn't mentioned on the post), entitled "Bribing the Bieber", and also the unaired promo and in-show segment of the special Shark Tank episode, while also answering every other question i had regarding this series and its timeline.
I was able to find the MP4 url of the missing episode "THE DOOF IS DUE" on the OG Disney video site, but it seems like it can't play the video as it's down. And the og youtube page also doesn't have the video indexed, meaning i reached a dead end. If anyone wants to help, i'd welcome it.
I now have an account. The situation is that the editor of the flash stuff didn't hear back from her end. My best bet is either to contact Disney or to find someone to spread awareness about this so i can get the attention of Disney and/or Povenmire(PnF Creator). However, i have no idea how to do either of those, any suggestions?