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

No, tractor beams don't affect range 3 bonuses. Agility never goes below 0 either.