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A- 'it' is always referring to the newspaper, the use of 'it' is grammatically correct
B-awful sentence; try to avoid the use of POSSESSIVE+GERUND (e.g. "..Graham's becoming.."; the parallelism is destroyed by the second part of the sentence: "it was...., and under..."
C-"having won" is awkward; the construction of the sentece after the comma is confussing
D-changes the meaning of the sentence (original sentence: the newspaper WON....; modified sentence: the newspaper IS WINNING..)
E-classic mistake of using an object pronoun ("HER command) to refer to a possessive noun ("KATHARINE GRAHAM's ...)