If my Lokix is Confused and successfully uses its "Jumping Shot" attack against my opponent's Mismagius ex with the "Swirling Prose" Ability, will the new Pokemon I send out be Confused?
No, it will not.
Jumping ShotSwirling Prose



×2
-30Swirling Prose
As long as this Pokémon is in the Active Spot, whenever your opponent's Active Pokémon moves to the Bench during their turn, their new Active Pokémon is now Confused.

Hexa-MagicYou may draw cards until you have 6 cards in your hand.
Pokémon ex rule
When your Pokémon ex is Knocked Out, your opponent takes 2 Prize cards.
If my Lokix is Confused and successfully uses its "Jumping Shot" attack against my opponent's Mismagius ex with the "Swirling Prose" Ability, will the new Pokemon I send out be Confused?
No, it will not.
If I have Mismagius ex with the "Swirling Prose" Ability active and I Knock Out the opponent's Active Pokemon, is the new Active Pokemon Confused?
No, because that replacement happens during your turn, not during theirs.