Running Comparative Evaluation of Reference Data: When Nimrod is attacked and would be hit, you may roll 2d6. If your roll is equal or higher than the attacker's attack roll, Nimrod evades that attack and after resolutions deal the attacker damage equal to their printed damage value.
Since, Running Comparative Evaluation of Reference Data is not an attack, the attacker would reduce damage by 2, but, not be able to roll a d6 to reduce damage taken to 0, correct?

Danger Room Construct: When Mister Sinister makes an attack, give him an Error token for each "1" in the attack roll (maximum 3). // If Mister Sinister has 2 or less Error tokens, characters take a maximum of 1 damage from Mister Sinister's attacks, Mister Sinister takes a maximum of 1 damage from opponent's attacks, and he can't be healed or chosen for Mastermind. Protected: Pulse Wave

Danger Room Construct: When Sabretooth makes an attack, after resolutions give him an Error token for each 1 in the attack roll (maximum 3). // If Sabretooth has 2 or less Error tokens, characters take a maximum of 1 damage from Sabretooth's attacks, Sabretooth takes a maximum of 1 damage from opponent's attacks, and he can't be healed or chosen for Mastermind. Protected: Pulse Wave.

Danger Room Construct: When Magneto makes an attack, give him an Error token for each "1" in the attack roll (maximum 3). // If Magneto has 2 or less Error tokens, characters take a maximum of 1 damage from Magneto's attacks, Magneto takes a maximum of 1 damage from opponent's attacks, and he can't be healed or chosen for Mastermind. Protected: Pulse Wave

If Mister Sinister, Sabretooth or Magneto have 2 or less Error tokens. Only Sabretooth's traited Toughness, could reduce damage dealt by a successful Running Comparative Evaluation of Reference Data, since, Danger Room Construct only triggers by an attack, correct?

Q1: Correct

Q2: In this specific case, yes (unless the other Danger Room constructs had a way to reduce damage). If Sabertooth was top dial, damage dealt would be 3 (his printed damage value). After reducers (Toughness), Sabertooth would take 2 damage, putting him on click #3. Since an attack value has to be equal to or greater than a defence value for a "hit" to happen (other than "becomes hit") (Determining Hits section on pg. 14 of the Rulebook), Sabertooth would not get to roll for his Super Senses because no attack is being made.

Yeah, the attacker is not being attacked and thus dealt damage. They are just dealt damage if they miss Nimrod (from his trit).

Nimrod is disgustingly good.

Magneto has Toughness, as well, it would reduce damage by 1, d'oh. If it wouldn't be for the Upcoming Sets and Rumors I'd be lost, it sucks not having dials easily accessible for XMAS.