Can I use Comfey's "Flower Selecting" Ability or Colress's Experiment if I have only 1 card left in my deck?
You can play either of them with only one card left in your deck; but you have to put the card into your hand, you cannot discard it or put it into the Lost Zone.
Source: TPCi Rules Team (2022-10-06)
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)