If an Imperial shots his Clusters 2X does that count as 2 seperate attacks for the sake of him using focus for only 3 dice or all six? And does the enemy roll his agility dice 2x.. one set of dice for each of the attacks?

Two separate attacks.

Yes, the focus only counts for one of the two attacks and the opponent gets to roll defense for each attack since that's one of the steps in making an attack.

Remember, spending a focus token causes you to physically change all focus results to hit results, thus it can only be used for the 3 dice currently being used for attack (granted the physically changing part can be shortcut and shenanigans happen when rolling more dice than you physically have). This applies to rerolls to. So if you have an x-wing with a target lock and a focus and you attack with the primary weapon, rolling one focus and two blanks, you should reroll the blanks before spending your focus… in that case, spending the focus first wiuld bot automatically cause future focus results from rerolling to be hits.