So I see that PermissionsEx overrides the entire OP system in 1.9.4 (which is an idea I can get behind). However, I'm using this mod in tandem with the Better Questing mod. To be able to edit quests, it requires a player to be an operator, so I'm wondering if there's a way to give a player OP still since pex blocks it and it doesn't have a way to tell the mod the player has all permissions.

You can go use the MC op commands using the /minecraft: prefix, which will add players to the server's ops list. However, it might make sense for the Better Questing mod to integrate with Sponge's permissions API (relatively simple -- if sponge is installed and you have a MC EntityPlayerMP object, you can just cast it -- so ((Player) mcPly).hasPermission("my.permission"); will tell the plugin whether or not a player has a certain permission.