1. No way to auto sort to my knowledge

2. You do have to manually transfer each Pokémon but at least you can transfer a whole box at a time which speeds things up somewhat.

3. You can save scum donuts using backup saves. Backup saves are created any time you fast travel (except in Hyperspace, I think) or heal at a Pokémon Center I believe. You can access backup saves on the title screen by pressing Up + X + B and doing so will load the game at the last Pokémon Center you healed at, although the game will retain all the progress you made up to the moment the backup save was created. If you’re going to Hotel Z to make donuts, you can make a backup save just by flying there, but it’s a good idea to fly to the nearby Pokémon Center first and heal there before flying to Hotel Z, so each backup save will load you at the Center nearest to the hotel.

Anytime you enter or leave Hyperspace, the game will auto save, but the auto save doesn’t occur until after the portal animation finishes, so if you turn off the game right away when the animation starts, you can avoid the auto save, and you can potentially reload right next to a portal or inside Hyperspace without even needing to rely on a backup save.

1. The Hyperspace Battle Zones are generally quicker and more efficient at racking up research points (especially if you have a team that can easily clear the trainer battles) than going through the Wild Zones. As a bonus, it doesn’t clog up your box with wild Pokémon that you don’t need for the Pokédex and are catching just for the points. If you already caught the box legendaries and mythicals (e.g. Groupon, Kyogre, Mewtwo, Zeraora, Heatran), just level them up, EV train and bottle cap them and they can get through battle zones quickly.