A tip for all those stuck between A & B ...
The computer software being designed for a project studying Native American access to higher education will not only meet the needs of that study, but also has the versatility and power of facilitating similar research endeavors.
(A) but also has the versatility and power of facilitating
(B) but also have the versatility and power to facilitate
Remove not only ... but also from the construction.
The software will meet the needs
and have the versatility
The same rule can be applied for any not only...but also constructions
Hope that helps.
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What are modifiers ??