this is a good question.
i go with E.
I'd go with E as well since the other choices have errors i can make out. Professor, would you please help us with the explanation though? I am not very clear on how the prepositional phrase "with almost half going" modifies "90000 tons"?
my reasoning is that the phrase "with..........." is not correct. so ABC are out. between D and E, D has "it", which doesot have a clear antecedent. therefore i eliminated it for E.
I liked "almost half of which going" in A, but the prepositional phrase "with........" does not sound good.