Any toughness-modifying effects, counters, Auras, or Equipment will apply after its toughness is set to the player's former life total. For example, say Tree of Perdition is equipped with Cultist's Staff (which makes it 2/15) and the player's life total is 7. After the exchange, Tree of Perdition would be a 2/9 creature (its toughness became 7, which was then modified by Cultist's Staff) and the player's life total would be 15.