So if I'm at range 2 and hit with a tractor beam then have ships fire at range 3 does the ghost get the additional die for range

I see it as range is the the first step decided in the combat phase so that is first on timing followed by any other dice modifications

So they get 1 for range 3 then lose it because the have -1 aglity for the rest of round

The calculation for number of green dice rolled is 'ship's agility with a minimum of zero, then add range and obstruction'.

Agility is calculated and that number is fed into the calculation of the number of attack dice.

So, a Ghost with 2 Structural Damage and a Tractor Token has 0-1-1=0 agility (because agility can't be below 0) to which range and obstruction and any other dice (e.g. from Zuckuss' pilot ability) are then added.

But Captain Kenkirk with Structural Damage assigned to him has 0+1 for his pilot ability-1 for Structural Damage=0 agility, then adds range and obstruction.

In short, yes, they do get the extra die for range 3 and any obstruction in this case.

Cheers for quick reply

Just to drive the point a bit further home, if you read the attack sequence in page 5 of rules reference, you'll notice that both obstruction and range 3 against primary weapon has "the defender rolls one additional defense die" and not "the defender increases his agility by one".