Moving from WMC to PLEX, need help converting WTV files to a more Plex friendly format

I’m finally moving away from Windows Media Center to full Plex solution. I already moved my movies to my new Unraid server and now I’m working on converting around 1400 WTV files and moving them to the server.

Does anyone have a guide or recommended settings on how best to do this to create a high quality recording that is Plex friendly and will play on an Apple TV or Roku later down the line?

I’ve tried a few test runs trying out HEVC (MP4) doing a custom rename on the files and having Comskip mark, but not remove the commercials (I’m paranoid about it removing part of the actual show). My first attempt didn’t show up in my Plex library, after I tweaked the rename string it showed up in Plex but for some reason it didn’t include the episode number in the title despite being a variable in the custom rename and Plex also didn’t generate a thumbnail. Should I skip HEVC and just use the MP4 normal or high quality presets? Are there specific MCEBuddy options I should be using to maximize Plex compatibility when converting from WTV?

This may help: