Denying that one of its many irregularities

Denying that one of its many irregularities had been the long-term mismanaging of company funds, the AD & M company produced clear evidence to back its claim.  

A.  its many irregularities had been the long-term
B.  its many irregularities has been the long-term
C.  its many irregularities is the long-term
D.  their many irregularities is the long-term
E.  their many irregularities had been the long-term

The best answer is A.  The singular pronoun its  agrees in number with the singular noun referent AD & M; the past perfect verb form had been is used appropriately to refer to an action completed prior to the action of the simple past tense produced.