Captain Jonus says:
When another friendly ship at range 1 attacks with a secondary weapon, it may reroll up to 2 attack dice.

Cluster Missiles says:

Attack [Target Lock]: Spend your target lock and discard this card to perform this attack twice.

Luke Skywalker says:

When defending, you may change 1 of your [focus] results to a [evade] result.

Situation:
Captain Jonus is within range 1 behind a Gamma Squadron Bomber that is equiped with a Cluster Missile. The Gamma Squadron pilot has a target lock and shoots at Luke Skywalker with Cluster Missiles.

Question 1:
Does the Gamma pilot get to reroll 2 attack dice once out of the Cluster Missile's 2 attacks of 3 attack dice?
Or
Does the Gamma pilot get to reroll 2 attack dice for each of the Cluster Missile's rolls of 3 attack dice each?

Question 2:
Does Luke Skywalker get to roll defense for each of the Cluster Missile attacks, and if so for each defense roll would he be allowed to change 1 [focus] to 1 [evade]?

(Based on what I understand, the Cluster Missiles count as 2 seperate attacks, so my guess has been the later, rerolling each attack of 3 dice).

Thanks for the responses and clarification!

Does the Gamma pilot get to reroll 2 attack dice for each of the Cluster Missile's rolls of 3 attack dice each?

This. It's two separate attacks in pretty much every way. So he'd effect both sets of attacks. Same way Marksmanship effects both the primary attack and the attack from Gunner/Luke.

Does Luke Skywalker get to roll defense for each of the Cluster Missile attacks, and if so for each defense roll would he be allowed to change 1 [focus] to 1 [evade]?

Same here, for the same reasons.

Jonus would allow you to reroll any or all of the 3 2 dice of the cluster missile attack for both attacks.

Luke would get to change one eye to an evade for each roll for defence he made against each attack.

* Jonus gives 2 dice only, not 3.

Jonus would allow you to reroll any or all of the 3 dice of the cluster missile attack for both attacks.

Not "or all" as Jonus only allows you to reroll up to 2 dice.