Should be C.
I think have is not correct here.The s/w will not only meet the needs, but it also has the versatility and power to facilitate.
We always say..
She has got a pen and a pencil.
She have got a pen and a pencil.
Plz correct me if I am wrong.
It should be B.
The computer software being designed for a project studying Native American assess to higher education will
not only meet the needs of that study,but also have
the versatility and power to facilitate...
since 'will' is being used , 'have' is required to maintain the right tense (simple future) for the second part of the sentence.