If I have a heavily damaged Basic Pokemon V in play, can I use Thorton to switch it with a regular one-prize Basic Pokemon from my discard pile?
Yes, and if the new Basic Pokemon has less HP than the amount of damage counters it is immediately KO'd and will relinquish only one prize to your opponent.
Source: TPCi Rules Team (2022-09-29)
If I have Comfey in play and I use its "Flower Selecting" Ability, can I then use Thorton to switch it with a different Comfey and use "Flower Selecting" from the new Comfey?
No, that won't work. Even though the new Comfey is a different Pokemon than the first one, it remembers the Flower Selecting Ability was already used this turn so you cannot use it again on that Pokemon.
Source: TPCi Rules Team (2022-09-29)
Can I use Thorton to put a non-Dark Basic Pokemon from my discard pile onto my bench if I have Eternatus VMAX with the "Eternal Zone" Ability in play?
No, you can't play Thorton at all if there aren't any Basic {D} Pokemon in your discard pile.
Source: TPCi Rules Team (2022-09-29)